Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 135709677
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: 135709677
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 13 of 438
Found at i:3578485 original size:15 final size:15
Alignment explanation
Indices: 3578465--3578495 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
3578455 CATATGAATA
3578465 ACTATTCCTAAAACG
1 ACTATTCCTAAAACG
3578480 ACTATTCCTAAAACG
1 ACTATTCCTAAAACG
3578495 A
1 A
3578496 GGTCAGCCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.42, C:0.26, G:0.06, T:0.26
Consensus pattern (15 bp):
ACTATTCCTAAAACG
Found at i:3582554 original size:32 final size:31
Alignment explanation
Indices: 3582507--3582595 Score: 90
Period size: 31 Copynumber: 2.8 Consensus size: 31
3582497 TTAAGTTCTC
* * *
3582507 TCAAACTTTTTAAAAATTCTCATTAATTTTT
1 TCAAAATTTTTAAAAATTCTAATTAAATTTT
* *
3582538 TCAAAATTTTTAAAAAATTGTAATCAAAATTTT
1 TCAAAATTTTT-AAAAATTCTAAT-TAAATTTT
* *
3582571 T-AAAAGTTTTAAAAATTCTTATTAA
1 TCAAAATTTTTAAAAATTCTAATTAA
3582596 GCCCCAAAAA
Statistics
Matches: 47, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
30 2 0.04
31 20 0.43
32 18 0.38
33 7 0.15
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.46
Consensus pattern (31 bp):
TCAAAATTTTTAAAAATTCTAATTAAATTTT
Found at i:3583478 original size:23 final size:23
Alignment explanation
Indices: 3583448--3583493 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
3583438 ATTGTTCAAA
3583448 AAAGTTACTTGAAAACTTTTCTT
1 AAAGTTACTTGAAAACTTTTCTT
3583471 AAAGTTACTTGAAAACTTTTCTT
1 AAAGTTACTTGAAAACTTTTCTT
3583494 CTTGTTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.43
Consensus pattern (23 bp):
AAAGTTACTTGAAAACTTTTCTT
Found at i:3583589 original size:45 final size:45
Alignment explanation
Indices: 3583525--3583610 Score: 163
Period size: 45 Copynumber: 1.9 Consensus size: 45
3583515 TCATGGGTCG
*
3583525 GGTAGCCTTGCTCGAAGGCCTGCCTGAAAAGTGAGATGGTTGTCA
1 GGTAGCCTTACTCGAAGGCCTGCCTGAAAAGTGAGATGGTTGTCA
3583570 GGTAGCCTTACTCGAAGGCCTGCCTGAAAAGTGAGATGGTT
1 GGTAGCCTTACTCGAAGGCCTGCCTGAAAAGTGAGATGGTT
3583611 TAGGCAAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.23, C:0.20, G:0.33, T:0.24
Consensus pattern (45 bp):
GGTAGCCTTACTCGAAGGCCTGCCTGAAAAGTGAGATGGTTGTCA
Found at i:3591250 original size:29 final size:29
Alignment explanation
Indices: 3591186--3591269 Score: 77
Period size: 30 Copynumber: 2.9 Consensus size: 29
3591176 TTATATATAG
3591186 TAAATTCTATTTTAATCCTTTAAAATAAA
1 TAAATTCTATTTTAATCCTTTAAAATAAA
* *
3591215 AATAATTCTA-TTTAATCCCTTT-AAATATGA
1 TA-AATTCTATTTTAAT-CCTTTAAAATA-AA
3591245 TAAATTAC-ATTTTAA-CCTTTCAAAA
1 TAAATT-CTATTTTAATCCTTT-AAAA
3591270 ATTTATAATT
Statistics
Matches: 45, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
28 5 0.11
29 17 0.38
30 23 0.51
ACGTcount: A:0.43, C:0.13, G:0.01, T:0.43
Consensus pattern (29 bp):
TAAATTCTATTTTAATCCTTTAAAATAAA
Found at i:3593707 original size:17 final size:17
Alignment explanation
Indices: 3593681--3593715 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
3593671 CAACCAATCA
3593681 AAAAGCGTCATGTCACT
1 AAAAGCGTCATGTCACT
*
3593698 AAAAGTGTCATGTCACT
1 AAAAGCGTCATGTCACT
3593715 A
1 A
3593716 TCTCATTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.26
Consensus pattern (17 bp):
AAAAGCGTCATGTCACT
Found at i:3593759 original size:24 final size:25
Alignment explanation
Indices: 3593731--3593790 Score: 95
Period size: 25 Copynumber: 2.4 Consensus size: 25
3593721 TTAAAATATA
*
3593731 ATTAAATAAAAAT-TTTATATTAAT
1 ATTAAATAAAAATAATTATATTAAT
*
3593755 ATTAAATAAAAATAATTGTATTAAT
1 ATTAAATAAAAATAATTATATTAAT
3593780 ATTAAATAAAA
1 ATTAAATAAAA
3593791 CAAAAAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
24 13 0.39
25 20 0.61
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (25 bp):
ATTAAATAAAAATAATTATATTAAT
Found at i:3594215 original size:40 final size:41
Alignment explanation
Indices: 3594161--3594247 Score: 104
Period size: 40 Copynumber: 2.1 Consensus size: 41
3594151 TATAATCAAT
*
3594161 TTTTATTATATTTTTTAATTTGTGTATTCTTTTAAGAATTG
1 TTTTAATATATTTTTTAATTTGTGTATTCTTTTAAGAATTG
* * * * * *
3594202 TTTTAATAT-TTTTTTTATTTGTTTCTTGTTTTAATATTTG
1 TTTTAATATATTTTTTAATTTGTGTATTCTTTTAAGAATTG
3594242 TTTTAA
1 TTTTAA
3594248 ATGTATTTGA
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
40 31 0.79
41 8 0.21
ACGTcount: A:0.22, C:0.02, G:0.08, T:0.68
Consensus pattern (41 bp):
TTTTAATATATTTTTTAATTTGTGTATTCTTTTAAGAATTG
Found at i:3600647 original size:23 final size:22
Alignment explanation
Indices: 3600571--3600722 Score: 137
Period size: 23 Copynumber: 6.5 Consensus size: 22
3600561 GACTTACCAT
3600571 AGCTCATATGAGCTTACCGATATATC
1 AGCTCATA-GAGCTTACCG-T-T-TC
** *
3600597 AGCTTGTAAGAGCTTACTGTTTTC
1 AGCTCAT-AGAGCTTACCG-TTTC
3600621 AGCTCATTAGAGCTTACCGTTTC
1 AGCTCA-TAGAGCTTACCGTTTC
*
3600644 AGCTCGTATGAGCTTA-C-TATTC
1 AGCTCATA-GAGCTTACCGT-TTC
3600666 AGCTCGATAGAGCTTACCGTTTC
1 AGCTC-ATAGAGCTTACCGTTTC
*
3600689 AGCTCGATAGATCTTACCGTTTC
1 AGCTC-ATAGAGCTTACCGTTTC
3600712 AGCTCAATAGA
1 AGCTC-ATAGA
3600723 TTATTGCTCA
Statistics
Matches: 108, Mismatches: 11, Indels: 17
0.79 0.08 0.12
Matches are distributed among these distances:
21 1 0.01
22 18 0.17
23 54 0.50
24 17 0.16
25 2 0.02
26 15 0.14
27 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.34
Consensus pattern (22 bp):
AGCTCATAGAGCTTACCGTTTC
Found at i:3600679 original size:45 final size:45
Alignment explanation
Indices: 3600571--3600722 Score: 157
Period size: 45 Copynumber: 3.2 Consensus size: 45
3600561 GACTTACCAT
* *
3600571 AGCTCATATGAGCTTACCGATATATCAGCTTGTAAGAGCTTACTGTTTTC
1 AGCTCATA-GAGCTTACCG-T-T-TCAGCTCGTAAGAGCTTAC-GTATTC
*
3600621 AGCTCATTAGAGCTTACCGTTTCAGCTCGTATGAGCTTAC-TATTC
1 AGCTCA-TAGAGCTTACCGTTTCAGCTCGTAAGAGCTTACGTATTC
*
3600666 AGCTCGATAGAGCTTACCGTTTCAGCTCG-ATAGATCTTACCGT-TTC
1 AGCTC-ATAGAGCTTACCGTTTCAGCTCGTA-AGAGCTTA-CGTATTC
3600712 AGCTCAATAGA
1 AGCTC-ATAGA
3600723 TTATTGCTCA
Statistics
Matches: 91, Mismatches: 6, Indels: 14
0.82 0.05 0.13
Matches are distributed among these distances:
44 1 0.01
45 37 0.41
46 15 0.16
47 18 0.20
48 1 0.01
49 1 0.01
50 16 0.18
51 2 0.02
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.34
Consensus pattern (45 bp):
AGCTCATAGAGCTTACCGTTTCAGCTCGTAAGAGCTTACGTATTC
Found at i:3602579 original size:23 final size:23
Alignment explanation
Indices: 3602497--3602583 Score: 92
Period size: 21 Copynumber: 4.0 Consensus size: 23
3602487 CCTGATCAGT
*
3602497 ATACGACACATAAAGTGCCT-AA
1 ATACGACACACAAAGTGCCTGAA
* *
3602519 A-ACGACACACGAGGTGCCTG--
1 ATACGACACACAAAGTGCCTGAA
* *
3602539 ATACGACACACGAGGTGCCTGAA
1 ATACGACACACAAAGTGCCTGAA
*
3602562 ATACGACACATAAAGTGCCTGA
1 ATACGACACACAAAGTGCCTGA
3602584 TCAGTAAAGC
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
20 1 0.02
21 34 0.62
22 1 0.02
23 19 0.35
ACGTcount: A:0.38, C:0.25, G:0.22, T:0.15
Consensus pattern (23 bp):
ATACGACACACAAAGTGCCTGAA
Found at i:3604146 original size:24 final size:25
Alignment explanation
Indices: 3604111--3604157 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
3604101 GCTCGAATGC
3604111 TTTTGTTCTCTTTTCTCTATTCTTT
1 TTTTGTTCTCTTTTCTCTATTCTTT
*
3604136 TTTTGTT-TCTTTTCTTTATTCT
1 TTTTGTTCTCTTTTCTCTATTCT
3604158 GTTTCTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.04, C:0.17, G:0.04, T:0.74
Consensus pattern (25 bp):
TTTTGTTCTCTTTTCTCTATTCTTT
Found at i:3604162 original size:18 final size:17
Alignment explanation
Indices: 3604130--3604166 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
3604120 CTTTTCTCTA
*
3604130 TTCTTTTTTTGTTTCTT
1 TTCTTTTTCTGTTTCTT
3604147 TTCTTTATTCTGTTTCTT
1 TTCTTT-TTCTGTTTCTT
3604165 TT
1 TT
3604167 ATTCACTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.03, C:0.14, G:0.05, T:0.78
Consensus pattern (17 bp):
TTCTTTTTCTGTTTCTT
Found at i:3604169 original size:14 final size:12
Alignment explanation
Indices: 3604119--3604170 Score: 52
Period size: 12 Copynumber: 4.2 Consensus size: 12
3604109 GCTTTTGTTC
*
3604119 TCTTTTCTCTAT
1 TCTTTTCTTTAT
*
3604131 TCTTTT-TTTGTT
1 TCTTTTCTTT-AT
3604143 TCTTTTCTTTAT
1 TCTTTTCTTTAT
3604155 TCTGTTTCTTTTAT
1 TCT-TTTC-TTTAT
3604169 TC
1 TC
3604171 ACTTTAGTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
11 2 0.06
12 17 0.52
13 7 0.21
14 7 0.21
ACGTcount: A:0.06, C:0.17, G:0.04, T:0.73
Consensus pattern (12 bp):
TCTTTTCTTTAT
Found at i:3607254 original size:6 final size:6
Alignment explanation
Indices: 3607229--3607267 Score: 51
Period size: 6 Copynumber: 6.2 Consensus size: 6
3607219 ATAATTTTGG
*
3607229 ATATAA ATATAGA TAAATAA ATATAA ATATAA ATATAA A
1 ATATAA ATATA-A -ATATAA ATATAA ATATAA ATATAA A
3607268 AAATCAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
6 23 0.79
7 2 0.07
8 4 0.14
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (6 bp):
ATATAA
Found at i:3613311 original size:29 final size:29
Alignment explanation
Indices: 3613274--3613330 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
3613264 ACTCACTATA
* *
3613274 TTATTATTAAACAAGTCCTTAACCTATTT
1 TTATAATTAAACAAGCCCTTAACCTATTT
* *
3613303 TTATAATTAAATAAGCCCTTAACTTATT
1 TTATAATTAAACAAGCCCTTAACCTATT
3613331 GTTTTTACTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.37, C:0.16, G:0.04, T:0.44
Consensus pattern (29 bp):
TTATAATTAAACAAGCCCTTAACCTATTT
Found at i:3617574 original size:28 final size:29
Alignment explanation
Indices: 3617543--3617599 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
3617533 CCTTCAACTC
* *
3617543 ACTA-TATTATTATTAAACAAGTCCTTAA
1 ACTATTATTATAATTAAACAAGCCCTTAA
* *
3617571 ACTATTTTTATAATTAAATAAGCCCTTAA
1 ACTATTATTATAATTAAACAAGCCCTTAA
3617600 CTTATGGTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 4 0.17
29 20 0.83
ACGTcount: A:0.42, C:0.14, G:0.04, T:0.40
Consensus pattern (29 bp):
ACTATTATTATAATTAAACAAGCCCTTAA
Found at i:3625637 original size:15 final size:15
Alignment explanation
Indices: 3625614--3625648 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
3625604 ATAACTTAAG
*
3625614 TTCAGTACTTAAATT
1 TTCAATACTTAAATT
3625629 TTCAATACTTAAATT
1 TTCAATACTTAAATT
3625644 TTCAA
1 TTCAA
3625649 CCTTATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.37, C:0.14, G:0.03, T:0.46
Consensus pattern (15 bp):
TTCAATACTTAAATT
Found at i:3629045 original size:57 final size:57
Alignment explanation
Indices: 3628887--3629050 Score: 208
Period size: 57 Copynumber: 2.9 Consensus size: 57
3628877 CATGTTAGAA
* * *
3628887 ATTTGAAGAAATGGTTGTCCAAAATGACTGTTGTTTTCATGATATATCATGTCTGAC
1 ATTTGAAGAAATGGTTGTCCAAAATGACTGTTGTTTTCATAATTTATTATGTCTGAC
* * * *
3628944 ATATGAAGAAATGATTG-CCTAAAATGGA-T-TCTGTTTCCAGAATTTATTATGTCTGAC
1 ATTTGAAGAAATGGTTGTCC-AAAAT-GACTGT-TGTTTTCATAATTTATTATGTCTGAC
*
3629001 ATTTGAAGAAATGGTTGTCCAAAATGACTGTTGTTTTTATAATTTATTAT
1 ATTTGAAGAAATGGTTGTCCAAAATGACTGTTGTTTTCATAATTTATTAT
3629051 CAAAGCTCAC
Statistics
Matches: 89, Mismatches: 12, Indels: 12
0.79 0.11 0.11
Matches are distributed among these distances:
56 5 0.06
57 79 0.89
58 5 0.06
ACGTcount: A:0.32, C:0.10, G:0.18, T:0.40
Consensus pattern (57 bp):
ATTTGAAGAAATGGTTGTCCAAAATGACTGTTGTTTTCATAATTTATTATGTCTGAC
Found at i:3630964 original size:20 final size:21
Alignment explanation
Indices: 3630939--3630982 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3630929 AGGTTTATTG
3630939 TTTTTATT-TCTTTTCTTCCT
1 TTTTTATTATCTTTTCTTCCT
* *
3630959 TTTTTATTATTTTTTCTTTCT
1 TTTTTATTATCTTTTCTTCCT
3630980 TTT
1 TTT
3630983 CAAAATTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.07, C:0.14, G:0.00, T:0.80
Consensus pattern (21 bp):
TTTTTATTATCTTTTCTTCCT
Found at i:3631708 original size:3 final size:3
Alignment explanation
Indices: 3631689--3632050 Score: 100
Period size: 3 Copynumber: 122.3 Consensus size: 3
3631679 TGGTTTAATG
* * *
3631689 TTA TTA -TA TTTA CTA TTA TTA TT- TTA CTA TTA TTA -TA TAA TATA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
* * * * * * *
3631733 TTT TTA TTA TCA TAA TTT TTA TTA TT- TTA CTA TTA TAA CTTAA CGTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TT-A -TTA
* * **
3631780 TTA TTA TTA CTA TTA TT- TTA TTT TTA TTA CCA TTA TTA TTA -TA CTT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
* * * ** *
3631826 GTA TT- TATA TTTA TT- TTA TT- CTA ATA CCA TTA TTG TTA TTA CTT-
1 TTA TTA T-TA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
* * *
3631870 CTA TTA TT- TT- TTAA CTA TTG TTA TTTA TATA TATA TTA TTA TTA TT-
1 TTA TTA TTA TTA TT-A TTA TTA TTA -TTA T-TA T-TA TTA TTA TTA TTA
* * * * * * *
3631916 TGTA TCA TTG TTA TTA TTA CTG TTA TTA ATA -TA CTTA TTA TTG CTA
1 T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA
* * *
3631962 TTA TTA TTT TTA CTA TTA TTA CTA TT- TTA TT- TT- TTA CTT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA
* * * *
3632004 TTA TTA TTA ATA TTA TTA TTA TTA TCA -TC TTA TT- TTA TTA CTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3632050 T
1 T
3632051 CATTGTTGTA
Statistics
Matches: 256, Mismatches: 70, Indels: 66
0.65 0.18 0.17
Matches are distributed among these distances:
2 35 0.14
3 190 0.74
4 27 0.11
5 4 0.02
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:3631716 original size:14 final size:15
Alignment explanation
Indices: 3631689--3631726 Score: 69
Period size: 14 Copynumber: 2.6 Consensus size: 15
3631679 TGGTTTAATG
3631689 TTATTATATTTACTA
1 TTATTATATTTACTA
3631704 TTATTAT-TTTACTA
1 TTATTATATTTACTA
3631718 TTATTATAT
1 TTATTATAT
3631727 AATATATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 14 0.64
15 8 0.36
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (15 bp):
TTATTATATTTACTA
Found at i:3631770 original size:23 final size:22
Alignment explanation
Indices: 3631702--3631770 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 22
3631692 TTATATTTAC
*
3631702 TATTATTATTTTACTATTATTA
1 TATTATTATTTTACTATTATAA
* * *
3631724 TATAATATATTTTTATTATCATAA
1 TATTAT-TA-TTTTACTATTATAA
*
3631748 TTTTTATTATTTTACTATTATAA
1 -TATTATTATTTTACTATTATAA
3631771 CTTAACGTAT
Statistics
Matches: 36, Mismatches: 8, Indels: 5
0.73 0.16 0.10
Matches are distributed among these distances:
22 5 0.14
23 14 0.39
24 13 0.36
25 4 0.11
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (22 bp):
TATTATTATTTTACTATTATAA
Found at i:3631796 original size:15 final size:15
Alignment explanation
Indices: 3631689--3632050 Score: 115
Period size: 15 Copynumber: 24.3 Consensus size: 15
3631679 TGGTTTAATG
3631689 TTATTA-TATTTACTA
1 TTATTATTA-TTACTA
3631704 TTATTATT-TTACTA
1 TTATTATTATTACTA
*
3631718 TTATTATATAATA-TA
1 TTATTAT-TATTACTA
* *
3631733 TTTTTATTATCA-TAA
1 TTATTATTATTACT-A
*
3631748 TTTTTATTATTTTACTA
1 TTATTATTA--TTACTA
*
3631765 TTATAACTTA--ACGTA
1 TTATTA-TTATTAC-TA
* *
3631780 TTATTATTACTATTA
1 TTATTATTATTACTA
* *
3631795 TTTTATTTTTATTACCA
1 --TTATTATTATTACTA
3631812 TTATTATTA-TACT-
1 TTATTATTATTACTA
3631825 TGTATT-TATATT--TA
1 T-TATTAT-TATTACTA
* *
3631839 TT-TTATTCTAATACCA
1 TTATTA-T-TATTACTA
*
3631855 TTATTGTTATTACT-
1 TTATTATTATTACTA
*
3631869 TCTATTATTTTTTAACTA
1 T-TATTA-TTATT-ACTA
*
3631887 TTGTTATT-TATA-TA
1 TTATTATTAT-TACTA
*
3631901 TATATTATTATTA-TT
1 T-TATTATTATTACTA
* * *
3631916 TGTATCATTGTTATTA
1 T-TATTATTATTACTA
* * *
3631932 TTACTGTTATTAATA
1 TTATTATTATTACTA
*
3631947 -TACTTATTATTGCTA
1 TTA-TTATTATTACTA
*
3631962 TTATTATTTTTACTA
1 TTATTATTATTACTA
*
3631977 TTATTACTA-T--T-
1 TTATTATTATTACTA
*
3631988 TTATT-TT-TTACTT
1 TTATTATTATTACTA
*
3632001 TTATTATTATTAATA
1 TTATTATTATTACTA
*
3632016 TTATTATTATTATCATC
1 TTATTATTATTA-C-TA
3632033 TTATT-TTATTACTA
1 TTATTATTATTACTA
3632047 TTAT
1 TTAT
3632051 CATTGTTGTA
Statistics
Matches: 258, Mismatches: 49, Indels: 81
0.66 0.13 0.21
Matches are distributed among these distances:
10 2 0.01
11 5 0.02
12 4 0.02
13 9 0.03
14 50 0.19
15 124 0.48
16 26 0.10
17 33 0.13
18 5 0.02
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.61
Consensus pattern (15 bp):
TTATTATTATTACTA
Found at i:3631798 original size:47 final size:46
Alignment explanation
Indices: 3631704--3631815 Score: 111
Period size: 47 Copynumber: 2.4 Consensus size: 46
3631694 ATATTTACTA
* * *
3631704 TTATTATTTTACTATTATTATATAATATATTTTTATTATCATAATTT
1 TTATTATTTTACTATTATAATATAACATATTATTATTATCATAA-TT
* *
3631751 TTATTATTTTACTATTATAACT-TAACGTATTATTATTA-CTATTATT
1 TTATTATTTTACTATTATAA-TATAACATATTATTATTATC-ATAATT
* *
3631797 TTATTTTTATTACCATTAT
1 TTATTATT-TTACTATTAT
3631816 TATTATACTT
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
46 10 0.18
47 44 0.80
48 1 0.02
ACGTcount: A:0.32, C:0.07, G:0.01, T:0.60
Consensus pattern (46 bp):
TTATTATTTTACTATTATAATATAACATATTATTATTATCATAATT
Found at i:3631806 original size:20 final size:21
Alignment explanation
Indices: 3631778--3631821 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
3631768 TAACTTAACG
*
3631778 TATTATTATTACTATTATT-T
1 TATTATTATTACCATTATTAT
*
3631798 TATTTTTATTACCATTATTAT
1 TATTATTATTACCATTATTAT
3631819 TAT
1 TAT
3631822 ACTTGTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.64
Consensus pattern (21 bp):
TATTATTATTACCATTATTAT
Found at i:3632331 original size:2 final size:2
Alignment explanation
Indices: 3632326--3632355 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3632316 ATATCTTTTA
3632326 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
3632356 TTATGTAATA
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:3632443 original size:24 final size:27
Alignment explanation
Indices: 3632396--3632452 Score: 75
Period size: 24 Copynumber: 2.2 Consensus size: 27
3632386 ACATTATTAT
3632396 TATTTCTAATATGTATATACTATGTAAA
1 TATTTCTAATATGTATATA-TATGTAAA
*
3632424 TATTTC-AATAT-TATAT-TATGTATA
1 TATTTCTAATATGTATATATATGTAAA
3632448 TATTT
1 TATTT
3632453 TTTATATATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 12 0.43
26 5 0.18
27 5 0.18
28 6 0.21
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.53
Consensus pattern (27 bp):
TATTTCTAATATGTATATATATGTAAA
Found at i:3635552 original size:19 final size:20
Alignment explanation
Indices: 3635504--3635547 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
3635494 TATAAGTTAC
3635504 TTAGCAAATTAAATATTTTT
1 TTAGCAAATTAAATATTTTT
3635524 TTAGCAAATTAAATATTTTT
1 TTAGCAAATTAAATATTTTT
3635544 TTAG
1 TTAG
3635548 TAATTTCCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.39, C:0.05, G:0.07, T:0.50
Consensus pattern (20 bp):
TTAGCAAATTAAATATTTTT
Found at i:3641740 original size:29 final size:28
Alignment explanation
Indices: 3641663--3641747 Score: 82
Period size: 29 Copynumber: 2.9 Consensus size: 28
3641653 AACATTAAAA
*
3641663 TAATATTAAAATCACTATATAAAAAAATTT
1 TAATATTAAAAT-AATATA-AAAAAAATTT
* *
3641693 CAATAAATAAAA-AATATAAAAAAAATTAT
1 TAAT-ATTAAAATAATATAAAAAAAATT-T
* *
3641722 TAATATTAAAATAAAATAAAATAAAT
1 TAATATTAAAATAATATAAAAAAAAT
3641748 ATAATTTTTT
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
28 15 0.33
29 21 0.47
30 3 0.07
31 6 0.13
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.31
Consensus pattern (28 bp):
TAATATTAAAATAATATAAAAAAAATTT
Found at i:3643017 original size:13 final size:13
Alignment explanation
Indices: 3642999--3643023 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3642989 CAACCGTAAA
3642999 TTTAACTAATTTT
1 TTTAACTAATTTT
3643012 TTTAACTAATTT
1 TTTAACTAATTT
3643024 AATCGATTTA
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:0.32, C:0.08, G:0.00, T:0.60
Consensus pattern (13 bp):
TTTAACTAATTTT
Found at i:3646482 original size:22 final size:21
Alignment explanation
Indices: 3646435--3646488 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
3646425 GGTTTTCCCT
*
3646435 TTTTTTATTTCTTTTTATTTA
1 TTTTTTATTTCTTTCTATTTA
* * *
3646456 ATTTTTCTTTCTTTCTTTCTTA
1 TTTTTTATTTCTTTCTAT-TTA
*
3646478 TTTTTTTTTTC
1 TTTTTTATTTC
3646489 ATCTTCTCCC
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
21 14 0.54
22 12 0.46
ACGTcount: A:0.09, C:0.11, G:0.00, T:0.80
Consensus pattern (21 bp):
TTTTTTATTTCTTTCTATTTA
Found at i:3646493 original size:25 final size:25
Alignment explanation
Indices: 3646442--3646493 Score: 61
Period size: 26 Copynumber: 2.1 Consensus size: 25
3646432 CCTTTTTTTA
*
3646442 TTTCTTTTTATTTAATTTTTCTTTC
1 TTTCTTTTTATTTAATTTTTCTATC
**
3646467 TTTCTTTCTTATTTTTTTTTTC-ATC
1 TTTCTTT-TTATTTAATTTTTCTATC
3646492 TT
1 TT
3646494 CTCCCTCCTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 11 0.48
26 12 0.52
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.77
Consensus pattern (25 bp):
TTTCTTTTTATTTAATTTTTCTATC
Found at i:3666389 original size:10 final size:10
Alignment explanation
Indices: 3666374--3666398 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
3666364 ATGTACTTAA
3666374 AATATAGATT
1 AATATAGATT
3666384 AATATAGATT
1 AATATAGATT
3666394 AATAT
1 AATAT
3666399 TTTTAATTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (10 bp):
AATATAGATT
Found at i:3670425 original size:26 final size:25
Alignment explanation
Indices: 3670396--3670451 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 25
3670386 AAATTTTAAT
*
3670396 TTTAATTAGAATATATTAAAAGAAAA
1 TTTAATTAAAATATATTAAAA-AAAA
*
3670422 TTTATTTAAAATATATTAAAAAAAA
1 TTTAATTAAAATATATTAAAAAAAA
*
3670447 GTTAA
1 TTTAA
3670452 AATGTTCTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
25 7 0.27
26 19 0.73
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (25 bp):
TTTAATTAAAATATATTAAAAAAAA
Found at i:3675092 original size:20 final size:19
Alignment explanation
Indices: 3675063--3675108 Score: 74
Period size: 20 Copynumber: 2.4 Consensus size: 19
3675053 AACTAATGGC
*
3675063 ATATATACATAATATATAT
1 ATATACACATAATATATAT
3675082 ATAATACACATAATATATAT
1 AT-ATACACATAATATATAT
3675102 ATATACA
1 ATATACA
3675109 TATTAGAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 7 0.28
20 18 0.72
ACGTcount: A:0.54, C:0.09, G:0.00, T:0.37
Consensus pattern (19 bp):
ATATACACATAATATATAT
Found at i:3675644 original size:11 final size:12
Alignment explanation
Indices: 3675628--3675664 Score: 60
Period size: 11 Copynumber: 3.2 Consensus size: 12
3675618 AGAAAAAAAA
3675628 GGAAGAGAG-AG
1 GGAAGAGAGAAG
3675639 GGAAGAGAGAAG
1 GGAAGAGAGAAG
3675651 GG-AGAGAGAAG
1 GGAAGAGAGAAG
3675662 GGA
1 GGA
3675665 GGGGGAAGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 20 0.83
12 4 0.17
ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (12 bp):
GGAAGAGAGAAG
Found at i:3675665 original size:11 final size:11
Alignment explanation
Indices: 3675626--3675675 Score: 57
Period size: 11 Copynumber: 4.5 Consensus size: 11
3675616 AAAGAAAAAA
*
3675626 AAGGAAGAGAG
1 AAGGGAGAGAG
3675637 -AGGGAAGAGAG
1 AAGGG-AGAGAG
3675648 AAGGGAGAGAG
1 AAGGGAGAGAG
* *
3675659 AAGGGAGGGGG
1 AAGGGAGAGAG
3675670 AAGGGA
1 AAGGGA
3675676 AATCCGGTCG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
10 3 0.09
11 27 0.79
12 4 0.12
ACGTcount: A:0.44, C:0.00, G:0.56, T:0.00
Consensus pattern (11 bp):
AAGGGAGAGAG
Found at i:3675955 original size:14 final size:14
Alignment explanation
Indices: 3675938--3675993 Score: 69
Period size: 14 Copynumber: 3.9 Consensus size: 14
3675928 TTTTGGTTTT
3675938 TTTTTTGCTGGAAA
1 TTTTTTGCTGGAAA
*
3675952 TTTTTTTCTGGAAA
1 TTTTTTGCTGGAAA
3675966 TTTTTTTTTGCTGG-AA
1 ---TTTTTTGCTGGAAA
3675982 TTTTTTGCTGGA
1 TTTTTTGCTGGA
3675994 TTTTTTTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
13 11 0.31
14 13 0.36
16 2 0.06
17 10 0.28
ACGTcount: A:0.16, C:0.07, G:0.20, T:0.57
Consensus pattern (14 bp):
TTTTTTGCTGGAAA
Found at i:3675970 original size:31 final size:30
Alignment explanation
Indices: 3675935--3676007 Score: 110
Period size: 30 Copynumber: 2.4 Consensus size: 30
3675925 TTTTTTTGGT
*
3675935 TTTTTTTTTGCTGGAAATTTTTTTCTGGAAA
1 TTTTTTTTTGCTGG-AATTTTTTGCTGGAAA
**
3675966 TTTTTTTTTGCTGGAATTTTTTGCTGGATT
1 TTTTTTTTTGCTGGAATTTTTTGCTGGAAA
3675996 TTTTTTTTTGCT
1 TTTTTTTTTGCT
3676008 TCCCCTCTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
30 25 0.64
31 14 0.36
ACGTcount: A:0.12, C:0.07, G:0.16, T:0.64
Consensus pattern (30 bp):
TTTTTTTTTGCTGGAATTTTTTGCTGGAAA
Found at i:3675999 original size:14 final size:15
Alignment explanation
Indices: 3675936--3676001 Score: 77
Period size: 13 Copynumber: 4.5 Consensus size: 15
3675926 TTTTTTGGTT
3675936 TTTTTTTTGCTGGAA
1 TTTTTTTTGCTGGAA
*
3675951 ATTTTTTT-CTGGAAA
1 TTTTTTTTGCTGG-AA
3675966 TTTTTTTTTGCTGGAA
1 -TTTTTTTTGCTGGAA
3675982 --TTTTTTGCTGG-A
1 TTTTTTTTGCTGGAA
3675994 TTTTTTTT
1 TTTTTTTT
3676002 TTTGCTTCCC
Statistics
Matches: 44, Mismatches: 2, Indels: 11
0.77 0.04 0.19
Matches are distributed among these distances:
12 1 0.02
13 11 0.25
14 10 0.23
15 9 0.20
16 9 0.20
17 4 0.09
ACGTcount: A:0.14, C:0.06, G:0.17, T:0.64
Consensus pattern (15 bp):
TTTTTTTTGCTGGAA
Found at i:3676447 original size:35 final size:35
Alignment explanation
Indices: 3676408--3676478 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
3676398 GGGGTGTGTG
3676408 ATGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGA
1 ATGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGA
3676443 ATGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGA
1 ATGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGA
3676478 A
1 A
3676479 GAGGCAAGTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.24, C:0.11, G:0.48, T:0.17
Consensus pattern (35 bp):
ATGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGA
Found at i:3677263 original size:48 final size:50
Alignment explanation
Indices: 3677187--3677333 Score: 183
Period size: 54 Copynumber: 2.9 Consensus size: 50
3677177 ATATGACCTA
**
3677187 AGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTGAAAAACAA-AA-
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAATAAC
* *
3677235 AGG-TACAACTCACCTCTCGCAATATGAGTTGCTTTTTGAAAGACAGAAATTAAC
1 AGGCT-CAACTCACCTCTCGCAATATGAGTTGATTTTTGAAA-A-A-CAA-TAAC
*
3677289 AGGCTCAACTCACCTCTCGCAATGTGAGTTGATTTTTGAAAAACA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACA
3677334 GGAATTGGAA
Statistics
Matches: 84, Mismatches: 7, Indels: 13
0.81 0.07 0.12
Matches are distributed among these distances:
47 1 0.01
48 36 0.43
49 1 0.01
50 1 0.01
51 3 0.04
52 1 0.01
53 3 0.04
54 37 0.44
55 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (50 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAATAAC
Found at i:3677569 original size:147 final size:140
Alignment explanation
Indices: 3677390--3677978 Score: 980
Period size: 147 Copynumber: 4.1 Consensus size: 140
3677380 TCAACTCACC
3677390 TATGAGTTGATTTTTGAAACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTC
1 TATGAGTTGA-TTTTGAAACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTC
* *
3677455 TCGCCATATGAGTTGATTTTGAAACATAAATTGAAAATTGAAATTACCTCAACGTGTTTTGAGGC
65 TCGCAATATGAGTTGATTTTGAAAC----A-T--AAATTGAAATTACCTCAACGTGTCTTGAGGC
3677520 TCAACTCACCTCTCGCAA
123 TCAACTCACCTCTCGCAA
*
3677538 TATGAGTTGATTTTGAAACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTTAACTCACCTCT
1 TATGAGTTGATTTTGAAACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCT
3677603 CGCAATATGAGTTGATTTTGAAACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCA
66 CGCAATATGAGTTGATTTTGAAACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCA
*
3677668 CCTCTCGCCA
131 CCTCTCGCAA
*
3677678 TATGAGTTGATTTTGAAACATAAATTGAAAATTGAAATTACCTCAACGTGTTTTGAGGCTCAACT
1 TATGAGTTGATTTTGAAAC----A-T--AAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACT
3677743 CACCTCTCGCAATATGAGTTGATTTTGAAACATAAATTGAAATTACCTCAACGTGTCTTGAGGCT
59 CACCTCTCGCAATATGAGTTGATTTTGAAACATAAATTGAAATTACCTCAACGTGTCTTGAGGCT
*
3677808 TAACTCACCTCTCGCAA
124 CAACTCACCTCTCGCAA
3677825 TATGAGTTGATTTTGAAACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCT
1 TATGAGTTGATTTTGAAACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCT
3677890 CGCAATATGAGTTGATTTTGAAACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCA
66 CGCAATATGAGTTGATTTTGAAACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCA
3677955 CCTCTCGCAA
131 CCTCTCGCAA
*
3677965 TGTGAGTTGATTTT
1 TATGAGTTGATTTT
3677979 CTGTCACTTG
Statistics
Matches: 423, Mismatches: 11, Indels: 22
0.93 0.02 0.05
Matches are distributed among these distances:
140 196 0.46
142 2 0.00
143 2 0.00
144 1 0.00
145 1 0.00
147 211 0.50
148 10 0.02
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (140 bp):
TATGAGTTGATTTTGAAACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCT
CGCAATATGAGTTGATTTTGAAACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCA
CCTCTCGCAA
Found at i:3677602 original size:70 final size:70
Alignment explanation
Indices: 3677489--3677978 Score: 863
Period size: 70 Copynumber: 6.9 Consensus size: 70
3677479 CATAAATTGA
*
3677489 AAATTGAAATTACCTCAACGTGTTTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGA
1 AAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGA
3677554 AACAT
66 AACAT
*
3677559 AAATTGAAATTACCTCAACGTGTCTTGAGGCTTAACTCACCTCTCGCAATATGAGTTGATTTTGA
1 AAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGA
3677624 AACAT
66 AACAT
*
3677629 AAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCCATATGAGTTGATTTTGA
1 AAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGA
3677694 AACATAAATT
66 AAC----A-T
*
3677704 GAAAATTGAAATTACCTCAACGTGTTTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
1 --AAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
3677769 GAAACAT
64 GAAACAT
*
3677776 AAATTGAAATTACCTCAACGTGTCTTGAGGCTTAACTCACCTCTCGCAATATGAGTTGATTTTGA
1 AAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGA
3677841 AACAT
66 AACAT
3677846 AAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGA
1 AAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGA
3677911 AACAT
66 AACAT
*
3677916 AAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATGTGAGTTGATTTT
1 AAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
3677979 CTGTCACTTG
Statistics
Matches: 403, Mismatches: 10, Indels: 14
0.94 0.02 0.03
Matches are distributed among these distances:
70 333 0.83
72 1 0.00
73 1 0.00
74 1 0.00
75 1 0.00
77 66 0.16
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (70 bp):
AAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGA
AACAT
Found at i:3677674 original size:217 final size:217
Alignment explanation
Indices: 3677390--3677978 Score: 1093
Period size: 217 Copynumber: 2.7 Consensus size: 217
3677380 TCAACTCACC
3677390 TATGAGTTGATTTTTGAAACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTC
1 TATGAGTTGA-TTTTGAAACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTC
3677455 TCGCCATATGAGTTGATTTTGAAACATAAATTGAAAATTGAAATTACCTCAACGTGTTTTGAGGC
65 TCGCCATATGAGTTGATTTTGAAACATAAATTGAAAATTGAAATTACCTCAACGTGTTTTGAGGC
3677520 TCAACTCACCTCTCGCAATATGAGTTGATTTTGAAACATAAATTGAAATTACCTCAACGTGTCTT
130 TCAACTCACCTCTCGCAATATGAGTTGATTTTGAAACATAAATTGAAATTACCTCAACGTGTCTT
3677585 GAGGCTTAACTCACCTCTCGCAA
195 GAGGCTTAACTCACCTCTCGCAA
3677608 TATGAGTTGATTTTGAAACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCT
1 TATGAGTTGATTTTGAAACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCT
3677673 CGCCATATGAGTTGATTTTGAAACATAAATTGAAAATTGAAATTACCTCAACGTGTTTTGAGGCT
66 CGCCATATGAGTTGATTTTGAAACATAAATTGAAAATTGAAATTACCTCAACGTGTTTTGAGGCT
3677738 CAACTCACCTCTCGCAATATGAGTTGATTTTGAAACATAAATTGAAATTACCTCAACGTGTCTTG
131 CAACTCACCTCTCGCAATATGAGTTGATTTTGAAACATAAATTGAAATTACCTCAACGTGTCTTG
3677803 AGGCTTAACTCACCTCTCGCAA
196 AGGCTTAACTCACCTCTCGCAA
3677825 TATGAGTTGATTTTGAAACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCT
1 TATGAGTTGATTTTGAAACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCT
* *
3677890 CGCAATATGAGTTGATTTTGAAAC----A-T--AAATTGAAATTACCTCAACGTGTCTTGAGGCT
66 CGCCATATGAGTTGATTTTGAAACATAAATTGAAAATTGAAATTACCTCAACGTGTTTTGAGGCT
*
3677948 CAACTCACCTCTCGCAATGTGAGTTGATTTT
131 CAACTCACCTCTCGCAATATGAGTTGATTTT
3677979 CTGTCACTTG
Statistics
Matches: 368, Mismatches: 3, Indels: 8
0.97 0.01 0.02
Matches are distributed among these distances:
210 61 0.17
212 1 0.00
213 1 0.00
217 295 0.80
218 10 0.03
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (217 bp):
TATGAGTTGATTTTGAAACATAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCACCTCT
CGCCATATGAGTTGATTTTGAAACATAAATTGAAAATTGAAATTACCTCAACGTGTTTTGAGGCT
CAACTCACCTCTCGCAATATGAGTTGATTTTGAAACATAAATTGAAATTACCTCAACGTGTCTTG
AGGCTTAACTCACCTCTCGCAA
Found at i:3694958 original size:31 final size:30
Alignment explanation
Indices: 3694886--3694958 Score: 92
Period size: 33 Copynumber: 2.3 Consensus size: 30
3694876 GTACTAAGAA
*
3694886 AAAATATATATATATATAAATAATAGTATT
1 AAAATATATATATATATAAATAATAATATT
* *
3694916 AGAAATCATATAGTATATATAACTGATAATATT
1 A-AAAT-ATATA-TATATATAAATAATAATATT
3694949 AAAATATATA
1 AAAATATATA
3694959 CATAATATTA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
30 1 0.03
31 9 0.24
32 9 0.24
33 18 0.49
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.37
Consensus pattern (30 bp):
AAAATATATATATATATAAATAATAATATT
Found at i:3695179 original size:3 final size:3
Alignment explanation
Indices: 3695171--3695412 Score: 149
Period size: 3 Copynumber: 78.0 Consensus size: 3
3695161 ACAAGGATAT
3695171 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
* * ** * * *
3695219 ATA ATA AT- ATA TTGA A-A CACA A-A AGCC ATT ATA ATA AAA ATA TTA
1 ATA ATA ATA ATA AT-A ATA -ATA ATA A-TA ATA ATA ATA ATA ATA ATA
* * * *
3695264 A-A ATA A-A GTA ATA GA-A ACA TTA CTA CAT- ATA TATA TATA CATA
1 ATA ATA ATA ATA ATA -ATA ATA ATA ATA -ATA ATA -ATA -ATA -ATA
* * * *
3695307 CATGA AGA TATA CACTA AT- GTA TTTCA ATA ACA ATA ATA ATA ATA ATA
1 -AT-A ATA -ATA -A-TA ATA ATA -AT-A ATA ATA ATA ATA ATA ATA ATA
3695355 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATAA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA
3695401 ATA ATA ATA ATA
1 ATA ATA ATA ATA
3695413 TTGAAATGCA
Statistics
Matches: 194, Mismatches: 25, Indels: 40
0.75 0.10 0.15
Matches are distributed among these distances:
2 12 0.06
3 150 0.77
4 28 0.14
5 4 0.02
ACGTcount: A:0.60, C:0.05, G:0.03, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:3696026 original size:11 final size:11
Alignment explanation
Indices: 3696010--3696049 Score: 71
Period size: 11 Copynumber: 3.5 Consensus size: 11
3696000 GGTAAATTTT
3696010 TTTTTTGTATA
1 TTTTTTGTATA
3696021 TTTTTTTGTATA
1 -TTTTTTGTATA
3696033 TTTTTTGTATA
1 TTTTTTGTATA
3696044 TTTTTT
1 TTTTTT
3696050 TTATGTTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
11 17 0.61
12 11 0.39
ACGTcount: A:0.15, C:0.00, G:0.07, T:0.78
Consensus pattern (11 bp):
TTTTTTGTATA
Found at i:3696040 original size:23 final size:22
Alignment explanation
Indices: 3696010--3696058 Score: 80
Period size: 23 Copynumber: 2.2 Consensus size: 22
3696000 GGTAAATTTT
3696010 TTTTTTGTATATTTTTTTGTATA
1 TTTTTTGTATATTTTTTT-TATA
*
3696033 TTTTTTGTATATTTTTTTTATG
1 TTTTTTGTATATTTTTTTTATA
3696055 TTTT
1 TTTT
3696059 AATATATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 7 0.28
23 18 0.72
ACGTcount: A:0.14, C:0.00, G:0.08, T:0.78
Consensus pattern (22 bp):
TTTTTTGTATATTTTTTTTATA
Found at i:3696058 original size:11 final size:12
Alignment explanation
Indices: 3696009--3696050 Score: 77
Period size: 12 Copynumber: 3.6 Consensus size: 12
3695999 AGGTAAATTT
3696009 TTTTTTTGTATA
1 TTTTTTTGTATA
3696021 TTTTTTTGTATA
1 TTTTTTTGTATA
3696033 -TTTTTTGTATA
1 TTTTTTTGTATA
3696044 TTTTTTT
1 TTTTTTT
3696051 TATGTTTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
11 11 0.38
12 18 0.62
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.79
Consensus pattern (12 bp):
TTTTTTTGTATA
Found at i:3696066 original size:23 final size:23
Alignment explanation
Indices: 3696017--3696067 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
3696007 TTTTTTTTTG
* *
3696017 TATATTTTTTTGTATATTTTTTG
1 TATATTTTTTTGTATATTTTATA
*
3696040 TATATTTTTTT-TATGTTTTAATA
1 TATATTTTTTTGTATATTTT-ATA
3696063 TATAT
1 TATAT
3696068 AGGTTAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 7 0.29
23 17 0.71
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (23 bp):
TATATTTTTTTGTATATTTTATA
Found at i:3696469 original size:35 final size:35
Alignment explanation
Indices: 3696429--3696499 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
3696419 GGAGTGTGTG
*
3696429 ATGGTGTTGGTGGCAGACAGCATGGGAGAATGGGA
1 ATGGTGCTGGTGGCAGACAGCATGGGAGAATGGGA
*
3696464 ATGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGA
1 ATGGTGCTGGTGGCAGACAGCATGGGAGAATGGGA
3696499 A
1 A
3696500 GAGGCAAGTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.25, C:0.10, G:0.46, T:0.18
Consensus pattern (35 bp):
ATGGTGCTGGTGGCAGACAGCATGGGAGAATGGGA
Found at i:3701566 original size:25 final size:27
Alignment explanation
Indices: 3701529--3701582 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 27
3701519 TCAAACATGC
3701529 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACACCTAGGGGT
* **
3701555 ATTTCGGT-AATTTTGCACCTAGGGGT
1 ATTTAGGTCAATTTAACACCTAGGGGT
3701581 AT
1 AT
3701583 AACAGTAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 6 0.25
26 18 0.75
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.37
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACACCTAGGGGT
Found at i:3701590 original size:26 final size:27
Alignment explanation
Indices: 3701546--3701621 Score: 82
Period size: 26 Copynumber: 2.8 Consensus size: 27
3701536 TCAATTTAAC
* * *
3701546 CCTAGGGGTATTTCGGTAATTTTGC-A
1 CCTAGGGGTATTACAGTAATTTTCCAA
*
3701572 CCTAGGGGTATAACAGTAATTTTCCATA
1 CCTAGGGGTATTACAGTAATTTTCCA-A
* *
3701600 CATAGGGGTATTATAGTAATTT
1 CCTAGGGGTATTACAGTAATTT
3701622 AGCTGCTTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
26 21 0.51
28 20 0.49
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.37
Consensus pattern (27 bp):
CCTAGGGGTATTACAGTAATTTTCCAA
Found at i:3704097 original size:26 final size:26
Alignment explanation
Indices: 3704010--3704143 Score: 218
Period size: 26 Copynumber: 5.2 Consensus size: 26
3704000 TGATACAAAT
3704010 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
3704036 TGATAAT-GGTTAGGTAAATGTT-CA
1 TGATAATAGGTTAGGTAAATGTTCCA
3704060 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
3704086 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
3704112 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
3704138 TGATAA
1 TGATAA
3704144 GAATTCATGT
Statistics
Matches: 104, Mismatches: 2, Indels: 4
0.95 0.02 0.04
Matches are distributed among these distances:
24 9 0.09
25 30 0.29
26 65 0.62
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.37
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:3711890 original size:22 final size:22
Alignment explanation
Indices: 3711865--3711906 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
3711855 ATATAAGTAC
* *
3711865 AATAACAATAATGGTAATAAAA
1 AATAAAAATAATAGTAATAAAA
3711887 AATAAAAATAATAGTAATAA
1 AATAAAAATAATAGTAATAA
3711907 TAGCACGTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.67, C:0.02, G:0.07, T:0.24
Consensus pattern (22 bp):
AATAAAAATAATAGTAATAAAA
Found at i:3712094 original size:14 final size:12
Alignment explanation
Indices: 3712060--3712107 Score: 60
Period size: 12 Copynumber: 3.8 Consensus size: 12
3712050 TGTTCATGCG
*
3712060 TAAATATAAAGA
1 TAAATATAAACA
*
3712072 TAGATATAATACA
1 TAAATATAA-ACA
3712085 TAAAATATAAACA
1 T-AAATATAAACA
3712098 TAAATATAAA
1 TAAATATAAA
3712108 GAGATAAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
12 17 0.55
13 7 0.23
14 7 0.23
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.27
Consensus pattern (12 bp):
TAAATATAAACA
Found at i:3712116 original size:26 final size:25
Alignment explanation
Indices: 3712060--3712117 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 25
3712050 TGTTCATGCG
* * *
3712060 TAAATATAAAGATAGATATAATACA
1 TAAATATAAACATAAATATAAGACA
*
3712085 TAAAATATAAACATAAATATAAAGAGA
1 T-AAATATAAACATAAATAT-AAGACA
3712112 TAAATA
1 TAAATA
3712118 AAATTAGATA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
25 1 0.04
26 21 0.78
27 5 0.19
ACGTcount: A:0.64, C:0.03, G:0.07, T:0.26
Consensus pattern (25 bp):
TAAATATAAACATAAATATAAGACA
Found at i:3712846 original size:18 final size:18
Alignment explanation
Indices: 3712825--3712865 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
3712815 TCGAAAATAA
3712825 AATAAAAAGGAAA-AAAAT
1 AATAAAAA-GAAAGAAAAT
*
3712843 AATAAATAGAAAGAAAAT
1 AATAAAAAGAAAGAAAAT
3712861 AATAA
1 AATAA
3712866 TAATGTAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 4 0.19
18 17 0.81
ACGTcount: A:0.76, C:0.00, G:0.10, T:0.15
Consensus pattern (18 bp):
AATAAAAAGAAAGAAAAT
Found at i:3712864 original size:21 final size:22
Alignment explanation
Indices: 3712824--3712868 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
3712814 TTCGAAAATA
3712824 AAATAAAAAGGAAAAAAATAAT
1 AAATAAAAAGGAAAAAAATAAT
* *
3712846 AAATAGAAA-GAAAATAATAAT
1 AAATAAAAAGGAAAAAAATAAT
3712867 AA
1 AA
3712869 TGTAATATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.16
Consensus pattern (22 bp):
AAATAAAAAGGAAAAAAATAAT
Found at i:3714799 original size:32 final size:32
Alignment explanation
Indices: 3714758--3714854 Score: 167
Period size: 32 Copynumber: 3.0 Consensus size: 32
3714748 AGCCCCCCAA
3714758 AAAAACCTAACCCAAAAAAAAAAAAAAAAAAG
1 AAAAACCTAACCCAAAAAAAAAAAAAAAAAAG
3714790 AAAAACCTAACCCAAAAAAAAAAGAAGAAAAAAG
1 AAAAACCTAACCCAAAAAAAAAA-AA-AAAAAAG
*
3714824 AAAAACCTAACCAAAAAAAAAAAAAAAAAAA
1 AAAAACCTAACCCAAAAAAAAAAAAAAAAAA
3714855 CCTAGCCACC
Statistics
Matches: 62, Mismatches: 1, Indels: 4
0.93 0.01 0.06
Matches are distributed among these distances:
32 29 0.47
33 4 0.06
34 29 0.47
ACGTcount: A:0.78, C:0.14, G:0.04, T:0.03
Consensus pattern (32 bp):
AAAAACCTAACCCAAAAAAAAAAAAAAAAAAG
Found at i:3724403 original size:71 final size:71
Alignment explanation
Indices: 3724295--3724446 Score: 225
Period size: 71 Copynumber: 2.1 Consensus size: 71
3724285 TTAATTTTTT
** * *
3724295 TTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAA
1 TTTTCAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAA
*
3724360 TTTTTG
66 TTTCTG
* *
3724366 TGTTTTAATTTCAACTCATATTGCGA-AGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCA
1 T-TTTCAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCA
3724430 ATTTCTG
65 ATTTCTG
3724437 TTTTCAATTT
1 TTTTCAATTT
3724447 ACGTTGTTCA
Statistics
Matches: 72, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
70 8 0.11
71 44 0.61
72 20 0.28
ACGTcount: A:0.23, C:0.16, G:0.22, T:0.39
Consensus pattern (71 bp):
TTTTCAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAA
TTTCTG
Found at i:3724556 original size:140 final size:140
Alignment explanation
Indices: 3724380--3725004 Score: 1132
Period size: 140 Copynumber: 4.5 Consensus size: 140
3724370 TTAATTTCAA
3724380 CTCATATTGCGA-AGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
3724444 TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTCTACTTTT
66 TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTCTACTTTT
3724509 TCAAAATCAG
131 TCAAAATCAG
3724519 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
*
3724584 TTTACGTTATTCAAGAATCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTCTACTTTT
66 TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTCTACTTTT
3724649 TCAAAATCAG
131 TCAAAATCAG
*
3724659 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTAAGGTATTTTCAATTT-TGTTTT-AA
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
*
3724722 TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAAGTGGGTTGAACCTTTTAATTTCTACTTTT
66 TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTCTACTTTT
3724787 TCAAAATCAG
131 TCAAAATCAG
*
3724797 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTATTTTCAA
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
*
3724862 TTTATGTTGTTCAAGAATCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTCTACTTTT
66 TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTCTACTTTT
3724927 TCAAAATCAG
131 TCAAAATCAG
*
3724937 CTCATATTGCGAGAGGTGAGTTGAGCCTC-GGTTCACATGCTGAAGTATTTTCAATTTCTGTCTT
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-TCAC--GCTGAGGTATTTTCAATTTCTGT-TT
3725001 TCAA
62 TCAA
3725005 AAAAAAAATT
Statistics
Matches: 469, Mismatches: 10, Indels: 10
0.96 0.02 0.02
Matches are distributed among these distances:
138 129 0.28
139 25 0.05
140 288 0.61
142 21 0.04
143 6 0.01
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.37
Consensus pattern (140 bp):
CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTCTACTTTT
TCAAAATCAG
Found at i:3724858 original size:13 final size:13
Alignment explanation
Indices: 3724840--3724864 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3724830 CACGCTGAGG
3724840 TATTTTCAATTTC
1 TATTTTCAATTTC
3724853 TATTTTCAATTT
1 TATTTTCAATTT
3724865 ATGTTGTTCA
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:0.24, C:0.12, G:0.00, T:0.64
Consensus pattern (13 bp):
TATTTTCAATTTC
Found at i:3724891 original size:278 final size:280
Alignment explanation
Indices: 3724380--3725004 Score: 1125
Period size: 278 Copynumber: 2.2 Consensus size: 280
3724370 TTAATTTCAA
*
3724380 CTCATATTGCGA-AGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAA
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTAAGGTATTTTCAATTTCTGTTTTCAA
*
3724444 TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTCTACTTTT
66 TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAAGTGGGTTGAACCTTTTAATTTCTACTTTT
3724509 TCAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTT
131 TCAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTT
*
3724574 CTGTTTTCAATTTACGTTATTCAAGAATCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAAT
196 CTATTTTCAATTTACGTTATTCAAGAATCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAAT
3724639 TTCTACTTTTTCAAAATCAG
261 TTCTACTTTTTCAAAATCAG
3724659 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTAAGGTATTTTCAATTT-TGTTTT-AA
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTAAGGTATTTTCAATTTCTGTTTTCAA
3724722 TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAAGTGGGTTGAACCTTTTAATTTCTACTTTT
66 TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAAGTGGGTTGAACCTTTTAATTTCTACTTTT
3724787 TCAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTT
131 TCAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTT
* *
3724852 CTATTTTCAATTTATGTTGTTCAAGAATCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAAT
196 CTATTTTCAATTTACGTTATTCAAGAATCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAAT
3724917 TTCTACTTTTTCAAAATCAG
261 TTCTACTTTTTCAAAATCAG
3724937 CTCATATTGCGAGAGGTGAGTTGAGCCTC-GGTTCACATGCTGAA-GTATTTTCAATTTCTGTCT
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-TCAC--GCT-AAGGTATTTTCAATTTCTGT-T
3725000 TTCAA
61 TTCAA
3725005 AAAAAAAATT
Statistics
Matches: 333, Mismatches: 5, Indels: 12
0.95 0.01 0.03
Matches are distributed among these distances:
277 2 0.01
278 246 0.74
279 18 0.05
280 57 0.17
281 5 0.02
282 3 0.01
283 2 0.01
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.37
Consensus pattern (280 bp):
CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTAAGGTATTTTCAATTTCTGTTTTCAA
TTTACGTTGTTCAAGAATCAACTCATATTGCGAGAAGTGGGTTGAACCTTTTAATTTCTACTTTT
TCAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTT
CTATTTTCAATTTACGTTATTCAAGAATCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAAT
TTCTACTTTTTCAAAATCAG
Found at i:3725131 original size:72 final size:73
Alignment explanation
Indices: 3725009--3725150 Score: 268
Period size: 72 Copynumber: 2.0 Consensus size: 73
3724999 TTTCAAAAAA
*
3725009 AAAATTTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTT
1 AAAATTTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAAATTCAATTT
3725074 CTGTTTTC
66 CTGTTTTC
3725082 AAAA-TTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAAATTCAATTT
1 AAAATTTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAAATTCAATTT
3725146 CTGTT
66 CTGTT
3725151 CAAAATGAGT
Statistics
Matches: 68, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
72 64 0.94
73 4 0.06
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32
Consensus pattern (73 bp):
AAAATTTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAAATTCAATTT
CTGTTTTC
Found at i:3725160 original size:49 final size:49
Alignment explanation
Indices: 3725104--3725199 Score: 174
Period size: 49 Copynumber: 2.0 Consensus size: 49
3725094 ATATTGCGAG
*
3725104 AAATGAGTTGAGCCTCAAGACACGTTGAGGTAAATTCAATTTCTGTTCA
1 AAATGAGTTGAGCCTCAAGACACGCTGAGGTAAATTCAATTTCTGTTCA
*
3725153 AAATGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTCTGTT
1 AAATGAGTTGAGCCTCAAGACACGCTGAGGTAAATTCAATTTCTGTT
3725200 TTCAAAATTC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (49 bp):
AAATGAGTTGAGCCTCAAGACACGCTGAGGTAAATTCAATTTCTGTTCA
Found at i:3725246 original size:121 final size:121
Alignment explanation
Indices: 3725032--3725271 Score: 426
Period size: 121 Copynumber: 2.0 Consensus size: 121
3725022 ATATTGCGAG
*
3725032 AAATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTCTGTTTTCAAAATTCAACTCATA
1 AAATGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTCTGTTTTCAAAATTCAACTCATA
*
3725097 TTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAAATTCAATTTCTGTTCA
66 TTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGTAAATTCAATTTCTGTTCA
3725153 AAATGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTCTGTTTTCAAAATTCAACTCATA
1 AAATGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTCTGTTTTCAAAATTCAACTCATA
* * **
3725218 TTGCGAGAAATTAGTTGAGCCTCAAGACATGCTGAGGTATTTTCAATTTCTGTT
66 TTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGTAAATTCAATTTCTGTT
3725272 TTTCAAAAAA
Statistics
Matches: 113, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
121 113 1.00
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (121 bp):
AAATGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTCTGTTTTCAAAATTCAACTCATA
TTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGTAAATTCAATTTCTGTTCA
Found at i:3725313 original size:78 final size:76
Alignment explanation
Indices: 3725153--3725506 Score: 452
Period size: 78 Copynumber: 4.7 Consensus size: 76
3725143 TTTCTGTTCA
* *
3725153 AAATGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTCTG-TTTTC---AAAATTCAACT
1 AAATGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTTCTGTTTTTCAAAAAAAATCAACT
3725214 CATATTGCGAG
66 CATATTGCGAG
* *
3725225 AAATTAGTTGAGCCTCAAGACATGCTGAGGTATTTTCAATTTCTGTTTTTCAAAAAAAAAATCAA
1 AAATGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTTCTGTTTTTC--AAAAAAAATCAA
*
3725290 CTCATATTGTGAG
64 CTCATATTGCGAG
*
3725303 AAATGAGTTGAGCCTCAAGACATGCTGAGGTATTTTCAATTTCTGTTTTT-AAAAAAAATCAACT
1 AAATGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTTCTGTTTTTCAAAAAAAATCAACT
3725367 CATATTGCGAG
66 CATATTGCGAG
** * * *
3725378 AGGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTCT-ATTGTC-AAAAAAATCAACT
1 AAATGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTTCTGTTTTTCAAAAAAAATCAACT
* **
3725441 CGTATTATGAG
66 CATATTGCGAG
*** * *
3725452 AGGCGAGTTGAGCCTCAGGTCACACGCCGAGGTATTTTCAATTTCTGTTTTTCAA
1 AAATGAGTTGAGCCTCAAG--ACACGCTGAGGTATTTTCAATTTCTGTTTTTCAA
3725507 TTTCTGCCTT
Statistics
Matches: 249, Mismatches: 22, Indels: 16
0.87 0.08 0.06
Matches are distributed among these distances:
72 42 0.17
73 5 0.02
74 41 0.16
75 64 0.26
76 23 0.09
77 4 0.02
78 70 0.28
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (76 bp):
AAATGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTTCTGTTTTTCAAAAAAAATCAACT
CATATTGCGAG
Found at i:3725433 original size:153 final size:148
Alignment explanation
Indices: 3725153--3725503 Score: 463
Period size: 153 Copynumber: 2.3 Consensus size: 148
3725143 TTTCTGTTCA
* * *
3725153 AAATGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTCTG-TTTTCAAAATTCAACTCAT
1 AAATGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTTCTGTTTTTAAAAAATCAACTCAT
* * * * *
3725217 ATTGCGAGAAATTAGTTGAGCCTCAAGACATGCTGAGGTATTTTCAATTTCTGTTTTTCAAAAAA
66 ATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTCTGATTGTC---AAA
*
3725282 AAAATCAACTCATATTGTGAG
128 AAAATCAACTCATATTATGAG
*
3725303 AAATGAGTTGAGCCTCAAGACATGCTGAGGTATTTTCAATTTCTGTTTTTAAAAAAAATCAACTC
1 AAATGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTTCTGTTTTT--AAAAAATCAACTC
**
3725368 ATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTCT-ATTGTCAAAA
64 ATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTCTGATTGTCAAAA
*
3725432 AAATCAACTCGTATTATGAG
129 AAATCAACTCATATTATGAG
*** * *
3725452 AGGCGAGTTGAGCCTCAGGTCACACGCCGAGGTATTTTCAATTTCTGTTTTT
1 AAATGAGTTGAGCCTCAAG--ACACGCTGAGGTATTTTCAATTTCTGTTTTT
3725504 CAATTTCTGC
Statistics
Matches: 177, Mismatches: 19, Indels: 9
0.86 0.09 0.04
Matches are distributed among these distances:
149 37 0.21
150 43 0.24
151 33 0.19
152 4 0.02
153 60 0.34
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.33
Consensus pattern (148 bp):
AAATGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTTCTGTTTTTAAAAAATCAACTCAT
ATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTCTGATTGTCAAAAAA
ATCAACTCATATTATGAG
Found at i:3725505 original size:14 final size:14
Alignment explanation
Indices: 3725486--3725512 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3725476 CGCCGAGGTA
3725486 TTTTCAATTTCTGT
1 TTTTCAATTTCTGT
3725500 TTTTCAATTTCTG
1 TTTTCAATTTCTG
3725513 CCTTTCAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.15, G:0.07, T:0.63
Consensus pattern (14 bp):
TTTTCAATTTCTGT
Found at i:3725518 original size:14 final size:14
Alignment explanation
Indices: 3725487--3725520 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
3725477 GCCGAGGTAT
**
3725487 TTTCAATTTCTGTT
1 TTTCAATTTCTGCC
3725501 TTTCAATTTCTGCC
1 TTTCAATTTCTGCC
3725515 TTTCAA
1 TTTCAA
3725521 AAAAAAAATC
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:0.18, C:0.21, G:0.06, T:0.56
Consensus pattern (14 bp):
TTTCAATTTCTGCC
Found at i:3725582 original size:94 final size:94
Alignment explanation
Indices: 3725428--3725600 Score: 231
Period size: 94 Copynumber: 1.8 Consensus size: 94
3725418 TTCTATTGTC
* * * *
3725428 AAAAAAATCAACTCGTATTATGAGAGGCGAGTTGAGCCTCAGGTCACACGCCGAGGTATTTTCAA
1 AAAAAAATCAACTCATATTACGAGAGGCGAGTTGAGCCTCAGCTCACACGCCGAGCTATTTTCAA
*
3725493 TTTCTGTTTTTCAATTTCTGCCTTTCAAA
66 TTTCTGTCTTTCAATTTCTGCCTTTCAAA
* * * * * *
3725522 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGTCT-TGACTCACGCGCTGAGCTATTTTCA
1 AAAAAAATCAACTCATATTACGAGAGGCGAGTTGAGCCTCAG-CTCACACGCCGAGCTATTTTCA
3725586 ATTTCTGTCTTTCAA
65 ATTTCTGTCTTTCAA
3725601 AAAAATCAAC
Statistics
Matches: 67, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
93 1 0.01
94 66 0.99
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (94 bp):
AAAAAAATCAACTCATATTACGAGAGGCGAGTTGAGCCTCAGCTCACACGCCGAGCTATTTTCAA
TTTCTGTCTTTCAATTTCTGCCTTTCAAA
Found at i:3725630 original size:77 final size:77
Alignment explanation
Indices: 3725500--3726090 Score: 316
Period size: 88 Copynumber: 7.2 Consensus size: 77
3725490 CAATTTCTGT
* *
3725500 TTTTCAATTTCTGCCTTTCAAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGTCTTGAC
1 TTTTCAATTTCTGTCTTTC---AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGAC
*
3725565 TCACGCGCTGAGCTA
63 TCACACGCTGAGCTA
3725580 TTTTCAATTTCTGTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAG-CTTCAGA-T
1 TTTTCAATTTCTGTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTT--GACT
* *
3725643 CACACACTGAGGTA
64 CACACGCTGAGCTA
* * * * * * **
3725657 TTTTTTCAATTTATATTTTTCAAAAAAATCAACTCACATTGCGAGATGTGAGTTGAGCCTCGGGT
1 --TTTTCAATTTCTGTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGACT
* *
3725722 CACATG-TCGAGGTA
64 CACACGCT-GAGCTA
* *** *
3725736 TTTTCAAAATCTATTTTTCAGATTCTGTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGA
1 TTTTC---A---A--TTTCTG--TCT-TTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGA
* **
3725801 GCCTTGGCTCACGTGCTGAGCTA
55 GCCTTGACTCACACGCTGAGCTA
* * *
3725824 TTTTCAATTTCTGTTTTTTTTCAAAAAAATTCAACTCATATTGCGAAAGGTGAGTTGAGCTTTTT
1 TTTTCAATTTCTG---TCTTTCAAAAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGC--CTT
* * * *
3725889 AATTTCTGCGAGA-GTTGAGTTGA
60 GA---CT-C-ACACGCTGAGCT-A
* * * * * *
3725912 GTCTTTTAATTTCTATTTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTTCAGT
1 -T-TTTCAATTTCTGTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGACT
** *
3725975 CACA-TATCGAGGTA
64 CACACGCT-GAGCTA
**
3725989 TTTTCAAAATCTG-CTTTTCAAGTTAAGTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTG
1 TTTTCAATTTCTGTC-TTTC------A-----AAAAAATCAACTCATATTGCGAGAGGTGAGTTG
* **
3726053 AGCCTTGGCTCACGTGCTGAGCTA
54 AGCCTTGACTCACACGCTGAGCTA
3726077 TTTTCAATTTCTGT
1 TTTTCAATTTCTGT
3726091 TTTTAATGTC
Statistics
Matches: 396, Mismatches: 67, Indels: 87
0.72 0.12 0.16
Matches are distributed among these distances:
75 12 0.03
76 4 0.01
77 57 0.14
78 9 0.02
79 62 0.16
80 33 0.08
81 31 0.08
82 4 0.01
83 3 0.01
84 28 0.07
85 9 0.02
86 2 0.01
87 15 0.04
88 114 0.29
89 3 0.01
90 10 0.03
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Consensus pattern (77 bp):
TTTTCAATTTCTGTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGACTCA
CACGCTGAGCTA
Found at i:3725711 original size:79 final size:76
Alignment explanation
Indices: 3725522--3725885 Score: 264
Period size: 79 Copynumber: 4.5 Consensus size: 76
3725512 GCCTTTCAAA
* *
3725522 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGTCTTGACTCACGCGCTGAGCTATTTTCAA
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAG-CTTGACTCACACACTGAGCTATTTTCAA
* *
3725587 TTTCTGTCTTTC
65 TTTATATCTTTC
*
3725599 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGA-TCACACACTGAGGTATTTTTT
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTT--GACTCACACACTGAGCTA--TTTT
*
3725663 CAATTTATATTTTTC
62 CAATTTATATCTTTC
* * * ** ** *
3725678 AAAAAAATCAACTCACATTGCGAGATGTGAGTTGAGCCTCGGGTCACA-TGTCGAGGTATTTTCA
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAG-CTTGACTCACACACT-GAGCTATTTTC-
* *
3725742 AAATCTATTTTTCAGATTCTGTTT
63 --A---A--TTT-ATA-TCT-TTC
** * * ***
3725766 TCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTATTTTCAA
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAG-CTTGACTCACACACTGAGCTATTTTCAA
* * *
3725831 TTTCTGTTTTTTTTC
65 -TT-T-ATATCTTTC
*
3725846 AAAAAAATTCAACTCATATTGCGAAAGGTGAGTTGAGCTT
1 AAAAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCTT
3725886 TTTAATTTCT
Statistics
Matches: 231, Mismatches: 35, Indels: 39
0.76 0.11 0.13
Matches are distributed among these distances:
76 3 0.01
77 53 0.23
78 4 0.02
79 61 0.26
80 13 0.06
81 32 0.14
82 2 0.01
83 1 0.00
85 4 0.02
86 2 0.01
87 2 0.01
88 53 0.23
89 1 0.00
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.35
Consensus pattern (76 bp):
AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTGACTCACACACTGAGCTATTTTCAAT
TTATATCTTTC
Found at i:3725908 original size:30 final size:30
Alignment explanation
Indices: 3725865--3725925 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
3725855 CAACTCATAT
3725865 TGCGAAAGGTGAGTTGAG-CTTTTTAATTTC
1 TGCGAAAGGTGAGTTGAGTC-TTTTAATTTC
* *
3725895 TGCGAGAGTTGAGTTGAGTCTTTTAATTTC
1 TGCGAAAGGTGAGTTGAGTCTTTTAATTTC
3725925 T
1 T
3725926 ATTTTTCAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 27 0.96
31 1 0.04
ACGTcount: A:0.21, C:0.10, G:0.26, T:0.43
Consensus pattern (30 bp):
TGCGAAAGGTGAGTTGAGTCTTTTAATTTC
Found at i:3725998 original size:253 final size:246
Alignment explanation
Indices: 3725280--3726094 Score: 799
Period size: 253 Copynumber: 3.3 Consensus size: 246
3725270 TTTTTCAAAA
* ** ** * *
3725280 AAAAAATCAACTCATATTGTGAGAAATGAGTTGAGCC-T--CAAGACATGCTGAGGTATTTTCAA
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGC-TCACGTGCTGAGCTATTTTCAA
* * * * *
3725342 TTTCTG---TTTTTAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCA-A-GACACG
65 TTTCTGTTTTTTTTCAAAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCTTCAGATCACACA
* * * ** ** * *
3725402 CTGAGGTA--ATTTCAATTTCTA-TTGTCAAAAAAATCAACTCGTATTATGAGAGGCGAGTTGAG
130 CTGAGGTATCTTTTCAATTTATATTTTTC-AAAAAATCAACTCACATTGCGAGAGGTGAGTTGAA
*** ** ** * **
3725464 CCTC-AGGTCACACGCCGAGGTATTTTCAATTTCTGTTTTTCAATTTCTGCCTTTC
194 CCTCGA-GTCACATATCGAGGTATTTTCAAAATCTACTTTTCAAGTTAAG--TTTC
* * *
3725519 AAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGTCTTGACTCACGCGCTGAGCTATTTT
1 ----AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTATTTT
* *
3725584 CAATTTCTG---TCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGATCAC
62 CAATTTCTGTTTTTTTTCAAAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCTTCAGATCAC
* *
3725646 ACACTGAGGTATTTTTTCAATTTATATTTTTCAAAAAAATCAACTCACATTGCGAGATGTGAGTT
127 ACACTGAGGTATCTTTTCAATTTATATTTTTC-AAAAAATCAACTCACATTGCGAGAGGTGAGTT
* * * * **
3725711 GAGCCTCGGGTCACATGTCGAGGTATTTTCAAAATCTATTTTTC-AGATTCTGTTTTC
191 GAACCTCGAGTCACATATCGAGGTATTTTCAAAATCTACTTTTCAAG-TTAAG-TTTC
*
3725768 -AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTATTTTCAAT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTATTTTCAAT
*
3725832 TTCTGTTTTTTTTCAAAAAAATTCAACTCATATTGCGAAAGGTGAGTTGAGCTTTTTA-ATTTCT
66 TTCTGTTTTTTTTCAAAAAAA-TCAACTCATATTGCGAAAGGTGAGTTGAGC--TTCAGA--TC-
* * * * * *
3725896 GCGAGAGTTGAGTTGAGTCTTTT-AATTTCTATTTTTC-AAAAATCAACTCATATTGCGAGAGGT
125 AC-ACA-CTGAGGT-A-TCTTTTCAATTTATATTTTTCAAAAAATCAACTCACATTGCGAGAGGT
*
3725959 GAGTTGAACCTTC-AGTCACATATCGAGGTATTTTCAAAATCTGCTTTTCAAGTTAAGTTTC
186 GAGTTGAACC-TCGAGTCACATATCGAGGTATTTTCAAAATCTACTTTTCAAGTTAAGTTTC
3726020 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTATTTTCAAT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTATTTTCAAT
3726085 TTCTGTTTTT
66 TTCTGTTTTT
3726095 AATGTCTGTT
Statistics
Matches: 492, Mismatches: 54, Indels: 42
0.84 0.09 0.07
Matches are distributed among these distances:
243 33 0.07
244 66 0.13
245 67 0.14
246 2 0.00
247 24 0.05
248 29 0.06
249 17 0.03
250 76 0.15
251 2 0.00
252 5 0.01
253 143 0.29
254 9 0.02
255 14 0.03
256 5 0.01
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.35
Consensus pattern (246 bp):
AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTCACGTGCTGAGCTATTTTCAAT
TTCTGTTTTTTTTCAAAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCTTCAGATCACACAC
TGAGGTATCTTTTCAATTTATATTTTTCAAAAAATCAACTCACATTGCGAGAGGTGAGTTGAACC
TCGAGTCACATATCGAGGTATTTTCAAAATCTACTTTTCAAGTTAAGTTTC
Found at i:3726803 original size:33 final size:33
Alignment explanation
Indices: 3726749--3726849 Score: 127
Period size: 33 Copynumber: 3.1 Consensus size: 33
3726739 TAAGCCCCCC
*
3726749 AAAA-AAAAACCTCACCC-AAAAAAAAAAAAGA
1 AAAAGAAAAACCTAACCCAAAAAAAAAAAAAGA
* *
3726780 AAAAGAAAAACTTAACCCAAAAAAAAAAGAAGAA
1 AAAAGAAAAACCTAACCCAAAAAAAAAAAAAG-A
* *
3726814 AAAAGAAAAACCTAA-CCAAAAAATAAAAAATA
1 AAAAGAAAAACCTAACCCAAAAAAAAAAAAAGA
3726846 AAAA
1 AAAA
3726850 AACCTAGCCA
Statistics
Matches: 60, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
31 4 0.07
32 16 0.27
33 25 0.42
34 15 0.25
ACGTcount: A:0.75, C:0.14, G:0.05, T:0.06
Consensus pattern (33 bp):
AAAAGAAAAACCTAACCCAAAAAAAAAAAAAGA
Found at i:3726834 original size:19 final size:18
Alignment explanation
Indices: 3726779--3726842 Score: 53
Period size: 19 Copynumber: 3.6 Consensus size: 18
3726769 AAAAAAAAAG
*
3726779 AAAAAGAAAAACTTAACCC
1 AAAAAGAAAAAC-TAACCA
* *
3726798 AAAAA-AAAAA-GAA-GA
1 AAAAAGAAAAACTAACCA
3726813 AAAAAGAAAAACCTAACCA
1 AAAAAGAAAAA-CTAACCA
*
3726832 AAAAATAAAAA
1 AAAAAGAAAAA
3726843 ATAAAAAAAC
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
15 5 0.14
16 7 0.20
18 7 0.20
19 16 0.46
ACGTcount: A:0.75, C:0.12, G:0.06, T:0.06
Consensus pattern (18 bp):
AAAAAGAAAAACTAACCA
Found at i:3726850 original size:33 final size:31
Alignment explanation
Indices: 3726749--3726850 Score: 116
Period size: 32 Copynumber: 3.1 Consensus size: 31
3726739 TAAGCCCCCC
* *
3726749 AAAA-AAAAACCTCACCCAAAAAAAAAAAAGA
1 AAAAGAAAAACCT-AACCAAAAAAAAAAAAAA
*
3726780 AAAAGAAAAACTTAACCCAAAAAAAAAAGAAGAA
1 AAAAGAAAAACCTAA-CCAAAAAAAAAA-AA-AA
3726814 AAAAGAAAAACCTAACCAAAAAATAAAAAATAA
1 AAAAGAAAAACCTAACCAAAAAA-AAAAAA-AA
3726847 AAAA
1 AAAA
3726851 ACCTAGCCAC
Statistics
Matches: 61, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
31 5 0.08
32 19 0.31
33 18 0.30
34 19 0.31
ACGTcount: A:0.75, C:0.14, G:0.05, T:0.06
Consensus pattern (31 bp):
AAAAGAAAAACCTAACCAAAAAAAAAAAAAA
Found at i:3726850 original size:34 final size:32
Alignment explanation
Indices: 3726749--3726851 Score: 118
Period size: 34 Copynumber: 3.1 Consensus size: 32
3726739 TAAGCCCCCC
* * *
3726749 AAAA-AAAAACCTCACCCAAAAAAAAAAAAGA
1 AAAAGAAAAACCTAACCAAAAAAAAAAAAAAA
* *
3726780 AAAAGAAAAACTTAACCCAAAAAAAAAAGAAGAA
1 AAAAGAAAAACCTAA-CCAAAAAAAAAA-AAAAA
3726814 AAAAGAAAAACCTAACCAAAAAATAAAAAATAAA
1 AAAAGAAAAACCTAACCAAAAAA-AAAAAA-AAA
3726848 AAAA
1 AAAA
3726852 CCTAGCCACC
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
31 4 0.07
32 8 0.13
33 21 0.35
34 27 0.45
ACGTcount: A:0.76, C:0.14, G:0.05, T:0.06
Consensus pattern (32 bp):
AAAAGAAAAACCTAACCAAAAAAAAAAAAAAA
Found at i:3728923 original size:30 final size:30
Alignment explanation
Indices: 3728883--3728943 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
3728873 TTACAAAGGC
*
3728883 ATTGGTGGTCTAGG-GGGTTTAGGCGGTGGA
1 ATTGGAGGTCTAGGTGGG-TTAGGCGGTGGA
*
3728913 ATTGGAGGTCTAGGTGGGTTAGGGGGTGGA
1 ATTGGAGGTCTAGGTGGGTTAGGCGGTGGA
3728943 A
1 A
3728944 CTGGTGGCGG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 25 0.89
31 3 0.11
ACGTcount: A:0.16, C:0.05, G:0.51, T:0.28
Consensus pattern (30 bp):
ATTGGAGGTCTAGGTGGGTTAGGCGGTGGA
Found at i:3728969 original size:42 final size:42
Alignment explanation
Indices: 3728915--3729010 Score: 165
Period size: 42 Copynumber: 2.3 Consensus size: 42
3728905 GCGGTGGAAT
*
3728915 TGGAGGTCTAGGTGGGTTAGGGGGTGGAACTGGTGGCGGAGG
1 TGGAGGTCTAGGTGGGTTAGGGGGTGGAACCGGTGGCGGAGG
* *
3728957 TGGAGGTCTAGGTGGTTTAGGGGGTGGAACCGGTGGCGGAGT
1 TGGAGGTCTAGGTGGGTTAGGGGGTGGAACCGGTGGCGGAGG
3728999 TGGAGGTCTAGG
1 TGGAGGTCTAGG
3729011 CAGTGGGACC
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.15, C:0.08, G:0.54, T:0.23
Consensus pattern (42 bp):
TGGAGGTCTAGGTGGGTTAGGGGGTGGAACCGGTGGCGGAGG
Found at i:3729022 original size:33 final size:33
Alignment explanation
Indices: 3728980--3729043 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
3728970 GGTTTAGGGG
*
3728980 GTGGAACCGGTGGCGGAGTTGGAGGTCTAGGCA
1 GTGGAACCGGGGGCGGAGTTGGAGGTCTAGGCA
*
3729013 GTGGGACCGGGGGCGGAGTTGGAGGTCTAGG
1 GTGGAACCGGGGGCGGAGTTGGAGGTCTAGG
3729044 TGGTGGTGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.16, C:0.14, G:0.53, T:0.17
Consensus pattern (33 bp):
GTGGAACCGGGGGCGGAGTTGGAGGTCTAGGCA
Found at i:3729127 original size:57 final size:57
Alignment explanation
Indices: 3729042--3729163 Score: 190
Period size: 57 Copynumber: 2.1 Consensus size: 57
3729032 TGGAGGTCTA
* * *
3729042 GGTGGTGGTGGTTGTCCAGGTACAGGTGGTGTAGGCAGTGAAGGTGGAGGTCTAGGT
1 GGTGGTGGTGGTTGTCCAGATACAGGTGGTGTAGGCAGTGAAGCTGGAGGTATAGGT
* * *
3729099 GGTGGTGGTGGTTGTCCAGATACCGGTGGTGTAGGCGGTGGAGCTGGAGGTATAGGT
1 GGTGGTGGTGGTTGTCCAGATACAGGTGGTGTAGGCAGTGAAGCTGGAGGTATAGGT
3729156 GGTGGTGG
1 GGTGGTGG
3729164 CAGCGGCGGA
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 59 1.00
ACGTcount: A:0.14, C:0.09, G:0.51, T:0.26
Consensus pattern (57 bp):
GGTGGTGGTGGTTGTCCAGATACAGGTGGTGTAGGCAGTGAAGCTGGAGGTATAGGT
Found at i:3730359 original size:30 final size:29
Alignment explanation
Indices: 3730315--3730379 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
3730305 TTAAAGCATT
* **
3730315 AAATTTATCGTTTTTATTTATTTTTAAAAA
1 AAATTTAGCGTTTTT-TAGATTTTTAAAAA
* *
3730345 TAATTTAGCTTTTTTTAGATTTTTAAAAA
1 AAATTTAGCGTTTTTTAGATTTTTAAAAA
3730374 AAATTT
1 AAATTT
3730380 CAGTAATTTG
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
29 17 0.59
30 12 0.41
ACGTcount: A:0.37, C:0.03, G:0.05, T:0.55
Consensus pattern (29 bp):
AAATTTAGCGTTTTTTAGATTTTTAAAAA
Found at i:3730577 original size:68 final size:66
Alignment explanation
Indices: 3730443--3730578 Score: 182
Period size: 68 Copynumber: 2.0 Consensus size: 66
3730433 ATATTTTATA
* * * * * *
3730443 AATATTTTAGTTTTTTATAATTTTTTAAGGGACCTATTTGCATATTTTCGAGACTGTCAATTACC
1 AATATTTTACTTTTTTATAATTTTTTAAGGGACCAATTTGCATATTTTCAAAACTATCAATGACC
3730508 C
66 C
* *
3730509 AATATTTTGACTTTTTTGATAATTTTTTAAGGGACCAATTTGCATTTTTTCAAAACTATCAGTGA
1 AATATTTT-ACTTTTTT-ATAATTTTTTAAGGGACCAATTTGCATATTTTCAAAACTATCAATGA
3730574 CCC
64 CCC
3730577 AA
1 AA
3730579 GAAATATTTA
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
66 8 0.13
67 7 0.12
68 45 0.75
ACGTcount: A:0.29, C:0.14, G:0.12, T:0.45
Consensus pattern (66 bp):
AATATTTTACTTTTTTATAATTTTTTAAGGGACCAATTTGCATATTTTCAAAACTATCAATGACC
C
Found at i:3732075 original size:47 final size:47
Alignment explanation
Indices: 3732020--3732113 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
3732010 TTACTCCGCC
3732020 CTGTTATAGATATTACCATCAGACACGAGTATGTTACTTGGATTACA
1 CTGTTATAGATATTACCATCAGACACGAGTATGTTACTTGGATTACA
3732067 CTGTTATAGATATTACCATCAGACACGAGTATGTTACTTGGATTACA
1 CTGTTATAGATATTACCATCAGACACGAGTATGTTACTTGGATTACA
3732114 ATGTGGGTGC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (47 bp):
CTGTTATAGATATTACCATCAGACACGAGTATGTTACTTGGATTACA
Found at i:3738638 original size:19 final size:18
Alignment explanation
Indices: 3738595--3738638 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
3738585 ATTTAAAATG
3738595 TTTA-TTAAAAATAAAAA
1 TTTATTTAAAAATAAAAA
*
3738612 TATAATTTAAAAATAAAAAA
1 T-TTATTTAAAAAT-AAAAA
3738632 TTTATTT
1 TTTATTT
3738639 GGACAATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 1 0.05
18 2 0.09
19 13 0.59
20 6 0.27
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
TTTATTTAAAAATAAAAA
Found at i:3740536 original size:23 final size:23
Alignment explanation
Indices: 3740509--3740554 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
3740499 TAAGATAATT
*
3740509 GGATTCAAATAATTTTGGGTTTA
1 GGATTCAAATAATTTTGGATTTA
* *
3740532 GGATTTAATTAATTTTGGATTTA
1 GGATTCAAATAATTTTGGATTTA
3740555 AATCTTTTCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.30, C:0.02, G:0.20, T:0.48
Consensus pattern (23 bp):
GGATTCAAATAATTTTGGATTTA
Found at i:3741034 original size:2 final size:2
Alignment explanation
Indices: 3740979--3741015 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3740969 TACTATAGAA
3740979 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
3741016 CATGATGTGT
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:3745065 original size:12 final size:12
Alignment explanation
Indices: 3745048--3745086 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
3745038 GTTATTAATA
3745048 TAATTTAGTTCT
1 TAATTTAGTTCT
3745060 TAATTTAGTTC-
1 TAATTTAGTTCT
3745071 TAATTT-GTT-T
1 TAATTTAGTTCT
3745081 TAATTT
1 TAATTT
3745087 TTTAATTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 9 0.35
11 6 0.23
12 11 0.42
ACGTcount: A:0.26, C:0.05, G:0.08, T:0.62
Consensus pattern (12 bp):
TAATTTAGTTCT
Found at i:3748697 original size:27 final size:28
Alignment explanation
Indices: 3748667--3748719 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
3748657 TATTTTATTT
3748667 ATATTAGGA-TAATTAATATTAAGATAA
1 ATATTAGGATTAATTAATATTAAGATAA
* *
3748694 ATATTAGGATTATTTAATTTTAAGAT
1 ATATTAGGATTAATTAATATTAAGAT
3748720 TTAATTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 9 0.39
28 14 0.61
ACGTcount: A:0.45, C:0.00, G:0.11, T:0.43
Consensus pattern (28 bp):
ATATTAGGATTAATTAATATTAAGATAA
Found at i:3748723 original size:13 final size:13
Alignment explanation
Indices: 3748705--3748729 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3748695 TATTAGGATT
3748705 ATTTAATTTTAAG
1 ATTTAATTTTAAG
3748718 ATTTAATTTTAA
1 ATTTAATTTTAA
3748730 TTATCTTTAT
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:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (13 bp):
ATTTAATTTTAAG
Found at i:3755146 original size:12 final size:12
Alignment explanation
Indices: 3755129--3755165 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
3755119 CAACCCAATC
3755129 TTTCTTTTTATT
1 TTTCTTTTTATT
3755141 TTTCTTTTTATT
1 TTTCTTTTTATT
*
3755153 TTTTTTTTTATT
1 TTTCTTTTTATT
3755165 T
1 T
3755166 ATTTTCCTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.08, C:0.05, G:0.00, T:0.86
Consensus pattern (12 bp):
TTTCTTTTTATT
Found at i:3755148 original size:6 final size:6
Alignment explanation
Indices: 3755133--3755210 Score: 56
Period size: 6 Copynumber: 12.7 Consensus size: 6
3755123 CCAATCTTTC
* *
3755133 TTTTTA TTTTTC TTTTTA TTTTTT TTTTTA TTTATT- TTCCTTTA TTTTCT-
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTT-TTA TT--TTTA TTTT-TA
3755183 TTTATTA TTTATTA -TTTTA -TTTTA TTTT
1 TTT-TTA TTT-TTA TTTTTA TTTTTA TTTT
3755211 AGTTAAATAT
Statistics
Matches: 60, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
5 8 0.13
6 36 0.60
7 13 0.22
8 3 0.05
ACGTcount: A:0.14, C:0.05, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTTTA
Found at i:3755154 original size:5 final size:5
Alignment explanation
Indices: 3755146--3755211 Score: 53
Period size: 5 Copynumber: 13.0 Consensus size: 5
3755136 TTATTTTTCT
* * * * * *
3755146 TTTTA TTTTT TTTTT TATTTA TTTTC CTTTA TTTTC TTTTA TTATT- TATTA
1 TTTTA TTTTA TTTTA T-TTTA TTTTA TTTTA TTTTA TTTTA TT-TTA TTTTA
3755197 TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA
3755212 GTTAAATATT
Statistics
Matches: 48, Mismatches: 10, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
4 2 0.04
5 40 0.83
6 6 0.12
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTTA
Found at i:3755158 original size:16 final size:17
Alignment explanation
Indices: 3755134--3755210 Score: 54
Period size: 16 Copynumber: 4.5 Consensus size: 17
3755124 CAATCTTTCT
3755134 TTTTATTTTTCTT-TTTA
1 TTTTATTTTT-TTATTTA
3755151 TTTT-TTTTTTTATTTA
1 TTTTATTTTTTTATTTA
* *
3755167 TTTTCCTTTATTTTCTTT-
1 TTTT-ATTT-TTTTATTTA
* *
3755185 TATTA-TTTATTATTTTA
1 TTTTATTTTTTTA-TTTA
3755202 TTTTATTTT
1 TTTTATTTT
3755211 AGTTAAATAT
Statistics
Matches: 47, Mismatches: 6, Indels: 13
0.71 0.09 0.20
Matches are distributed among these distances:
15 5 0.11
16 18 0.38
17 8 0.17
18 9 0.19
19 7 0.15
ACGTcount: A:0.14, C:0.05, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTTATTTTTTTATTTA
Found at i:3756372 original size:118 final size:118
Alignment explanation
Indices: 3756183--3756512 Score: 606
Period size: 118 Copynumber: 2.8 Consensus size: 118
3756173 TACAGCTTAG
*
3756183 ATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATTCTACTTCGCGTCAAAAGGT
1 ATCGTGACTGACTGAGTAATCGGGGTAGGGTGCTTGGGTTGTCATTCTACTTCGCGTCAAAAGGT
3756248 TGTGTGGCGTGACAAGTAAAACTCCGCTAGCCGAGGTTATGGGTATGGCTCAA
66 TGTGTGGCGTGACAAGTAAAACTCCGCTAGCCGAGGTTATGGGTATGGCTCAA
3756301 ATCGTGACTGACTGAGTAATCGGGGTAGGGTGCTTGGGTTGTCATTCTACTTCGCGTCAAAAGGT
1 ATCGTGACTGACTGAGTAATCGGGGTAGGGTGCTTGGGTTGTCATTCTACTTCGCGTCAAAAGGT
3756366 TGTGTGGCGTGACAAGTAAAACTCCGCTAGCCGAGGTTATGGGTATGGCTCAA
66 TGTGTGGCGTGACAAGTAAAACTCCGCTAGCCGAGGTTATGGGTATGGCTCAA
3756419 ATCGTGACTGACTGAGTAATCGGGGTAGGGTGCTTGGGTTGTCATTCTACTTCGCGTCAAAAGGT
1 ATCGTGACTGACTGAGTAATCGGGGTAGGGTGCTTGGGTTGTCATTCTACTTCGCGTCAAAAGGT
* ****
3756484 TGTGTGACGTGTTGGGTAAAACTCCGCTA
66 TGTGTGGCGTGACAAGTAAAACTCCGCTA
3756513 ACCGGAAATA
Statistics
Matches: 206, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
118 206 1.00
ACGTcount: A:0.22, C:0.18, G:0.32, T:0.28
Consensus pattern (118 bp):
ATCGTGACTGACTGAGTAATCGGGGTAGGGTGCTTGGGTTGTCATTCTACTTCGCGTCAAAAGGT
TGTGTGGCGTGACAAGTAAAACTCCGCTAGCCGAGGTTATGGGTATGGCTCAA
Found at i:3756648 original size:7 final size:7
Alignment explanation
Indices: 3756638--3756677 Score: 53
Period size: 7 Copynumber: 5.6 Consensus size: 7
3756628 AATAAAATTT
3756638 AAAAAGA
1 AAAAAGA
3756645 AAAAAGA
1 AAAAAGA
*
3756652 AAAAATCA
1 AAAAA-GA
3756660 AAAAAGA
1 AAAAAGA
*
3756667 AAGAAGA
1 AAAAAGA
3756674 AAAA
1 AAAA
3756678 TAAGTGCTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 22 0.79
8 6 0.21
ACGTcount: A:0.82, C:0.03, G:0.12, T:0.03
Consensus pattern (7 bp):
AAAAAGA
Found at i:3756656 original size:15 final size:14
Alignment explanation
Indices: 3756638--3756677 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
3756628 AATAAAATTT
3756638 AAAAAGAAAAAAGA
1 AAAAAGAAAAAAGA
*
3756652 AAAAATCAAAAAAGA
1 AAAAA-GAAAAAAGA
*
3756667 AAGAAGAAAAA
1 AAAAAGAAAAA
3756678 TAAGTGCTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.82, C:0.03, G:0.12, T:0.03
Consensus pattern (14 bp):
AAAAAGAAAAAAGA
Found at i:3757330 original size:10 final size:10
Alignment explanation
Indices: 3757311--3757342 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
3757301 TTTTAGGATT
3757311 TTAT-TTTAA
1 TTATCTTTAA
3757320 TTATCTTTAA
1 TTATCTTTAA
3757330 TTATCTTTAA
1 TTATCTTTAA
3757340 TTA
1 TTA
3757343 AATGTATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 4 0.18
10 18 0.82
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.62
Consensus pattern (10 bp):
TTATCTTTAA
Found at i:3762563 original size:27 final size:27
Alignment explanation
Indices: 3762532--3762618 Score: 88
Period size: 26 Copynumber: 3.2 Consensus size: 27
3762522 TTTACAATAC
* *
3762532 TATATTTTTTAATACCATATTATTATA
1 TATATTTTTTAATACTATATTATTGTA
* *
3762559 TATA-TTCTTAATATTATA-TATTGTA
1 TATATTTTTTAATACTATATTATTGTA
*
3762584 TGTATTTTCTTAATAACTATATTATATGTA
1 TATATTTT-TTAAT-ACTATATTAT-TGTA
3762614 TATAT
1 TATAT
3762619 ATAGTATGTA
Statistics
Matches: 47, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
25 9 0.19
26 13 0.28
27 9 0.19
28 5 0.11
29 3 0.06
30 8 0.17
ACGTcount: A:0.36, C:0.06, G:0.03, T:0.55
Consensus pattern (27 bp):
TATATTTTTTAATACTATATTATTGTA
Found at i:3765044 original size:12 final size:13
Alignment explanation
Indices: 3765027--3765063 Score: 60
Period size: 12 Copynumber: 3.0 Consensus size: 13
3765017 CTTCCTTCTA
3765027 GCCTCAT-CCTTT
1 GCCTCATACCTTT
3765039 GCCTCATACC-TT
1 GCCTCATACCTTT
3765051 GCCTCATACCTTT
1 GCCTCATACCTTT
3765064 CAATGACGCG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 19 0.83
13 4 0.17
ACGTcount: A:0.14, C:0.41, G:0.08, T:0.38
Consensus pattern (13 bp):
GCCTCATACCTTT
Found at i:3766343 original size:18 final size:20
Alignment explanation
Indices: 3766307--3766343 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3766297 TAATTATTTT
*
3766307 TTATATAATTAAATTAATAA
1 TTATATAATTAAATAAATAA
3766327 TTATATAA-TAAA-AAATA
1 TTATATAATTAAATAAATA
3766344 TAATTTTGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 4 0.25
19 4 0.25
20 8 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
TTATATAATTAAATAAATAA
Found at i:3768332 original size:31 final size:31
Alignment explanation
Indices: 3768297--3768357 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
3768287 CATAAGTGGA
*
3768297 GATAGATAGAGACGATGGTCTTGACATAGTT
1 GATAGATAGAGACAATGGTCTTGACATAGTT
3768328 GATAGATAGAGACAATGGTCTTGACATAGT
1 GATAGATAGAGACAATGGTCTTGACATAGT
3768358 GTTCGTTTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.34, C:0.10, G:0.28, T:0.28
Consensus pattern (31 bp):
GATAGATAGAGACAATGGTCTTGACATAGTT
Found at i:3773475 original size:12 final size:12
Alignment explanation
Indices: 3773458--3773490 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
3773448 CGGCCCACCC
3773458 ATATTAATTTTT
1 ATATTAATTTTT
3773470 ATATT-ATTTTT
1 ATATTAATTTTT
3773481 ATA-TAATTTT
1 ATATTAATTTT
3773491 AAAAAATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 14 0.70
12 5 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:3773515 original size:18 final size:18
Alignment explanation
Indices: 3773492--3773531 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
3773482 TATAATTTTA
*
3773492 AAAAATA-TATAATACATC
1 AAAAATACTA-AAAACATC
3773510 AAAAATACTAAAAACATC
1 AAAAATACTAAAAACATC
3773528 AAAA
1 AAAA
3773532 TAAATATTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 18 0.90
19 2 0.10
ACGTcount: A:0.68, C:0.12, G:0.00, T:0.20
Consensus pattern (18 bp):
AAAAATACTAAAAACATC
Found at i:3773649 original size:30 final size:30
Alignment explanation
Indices: 3773614--3773670 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
3773604 TTTAACAAGT
*
3773614 AAATATCTCTAAAATAATAACAAAATTAAC
1 AAATATCTCTAAAATAACAACAAAATTAAC
* *
3773644 AAATATTTTTAAAATAACAACAAAATT
1 AAATATCTCTAAAATAACAACAAAATT
3773671 GATAATAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.60, C:0.11, G:0.00, T:0.30
Consensus pattern (30 bp):
AAATATCTCTAAAATAACAACAAAATTAAC
Found at i:3773737 original size:22 final size:23
Alignment explanation
Indices: 3773701--3773752 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
3773691 ACAATTTTCA
3773701 AATAATAATAATAAAAT-AGTAGC
1 AATAATAATAATAAAATGA-TAGC
*
3773724 AATAA-AATACTAAAATGATAGC
1 AATAATAATAATAAAATGATAGC
3773746 AA-AATAA
1 AATAATAA
3773753 GGAGAAAACA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 2 0.08
22 18 0.69
23 6 0.23
ACGTcount: A:0.63, C:0.06, G:0.08, T:0.23
Consensus pattern (23 bp):
AATAATAATAATAAAATGATAGC
Found at i:3778481 original size:20 final size:20
Alignment explanation
Indices: 3778456--3778493 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
3778446 AAACTACGTC
3778456 GTTTACTAGTTAAATAATTT
1 GTTTACTAGTTAAATAATTT
3778476 GTTTACTAGTTAAATAAT
1 GTTTACTAGTTAAATAAT
3778494 CAATCCATGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.05, G:0.11, T:0.47
Consensus pattern (20 bp):
GTTTACTAGTTAAATAATTT
Found at i:3780830 original size:28 final size:29
Alignment explanation
Indices: 3780780--3780836 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
3780770 AAATCCCCTA
* * *
3780780 TTTACTAAAAAAAGTAATTGAAAATATAT
1 TTTACTAAAAAAAATAATGGAAAAAATAT
*
3780809 TTTAC-AAAAAAAATTATGGAAAAAATAT
1 TTTACTAAAAAAAATAATGGAAAAAATAT
3780837 ATAATATTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 19 0.79
29 5 0.21
ACGTcount: A:0.58, C:0.04, G:0.07, T:0.32
Consensus pattern (29 bp):
TTTACTAAAAAAAATAATGGAAAAAATAT
Found at i:3790061 original size:21 final size:20
Alignment explanation
Indices: 3790006--3790062 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 20
3789996 GAAAATAATT
* *
3790006 AAAATTAATAAATAATTATAG
1 AAAATT-ATAAAAAAGTATAG
* *
3790027 AAATTTACATAAAAAGTATAG
1 AAAATTATA-AAAAAGTATAG
3790048 AAAATTATTAAAAAA
1 AAAATTA-TAAAAAA
3790063 CCAGAAAAGT
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
20 2 0.07
21 25 0.89
22 1 0.04
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.30
Consensus pattern (20 bp):
AAAATTATAAAAAAGTATAG
Found at i:3790089 original size:19 final size:20
Alignment explanation
Indices: 3790067--3790124 Score: 59
Period size: 19 Copynumber: 3.0 Consensus size: 20
3790057 AAAAAACCAG
3790067 AAAAGTATAAA-AATTGTAA
1 AAAAGTATAAAGAATTGTAA
* *
3790086 AAAAATATAAAGAAAT-TAA
1 AAAAGTATAAAGAATTGTAA
* *
3790105 AAATG-ATAAATAATTGTAA
1 AAAAGTATAAAGAATTGTAA
3790124 A
1 A
3790125 TAATTAAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
18 8 0.26
19 20 0.65
20 3 0.10
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.26
Consensus pattern (20 bp):
AAAAGTATAAAGAATTGTAA
Found at i:3791127 original size:3 final size:3
Alignment explanation
Indices: 3791119--3791169 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
3791109 TTTCATACTT
3791119 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3791167 TAA
1 TAA
3791170 CTGCATATAT
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:3791506 original size:18 final size:18
Alignment explanation
Indices: 3791483--3791526 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
3791473 AATAATTTTT
3791483 TTTTAATATTTAAAAATA
1 TTTTAATATTTAAAAATA
* *
3791501 TTTTAATATTTTATAATA
1 TTTTAATATTTAAAAATA
3791519 TTTTAATA
1 TTTTAATA
3791527 ATTTTTATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTTAATATTTAAAAATA
Found at i:3791517 original size:10 final size:10
Alignment explanation
Indices: 3791481--3791535 Score: 53
Period size: 10 Copynumber: 5.7 Consensus size: 10
3791471 GCAATAATTT
*
3791481 TTTTTTAATA
1 TTTTATAATA
* *
3791491 TTTAAAAATA
1 TTTTATAATA
3791501 -TTT-TAATA
1 TTTTATAATA
3791509 TTTTATAATA
1 TTTTATAATA
3791519 TTTTAATAAT-
1 TTTT-ATAATA
3791529 TTTTATA
1 TTTTATA
3791536 TAGTTTTTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
8 4 0.11
9 8 0.22
10 20 0.54
11 5 0.14
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (10 bp):
TTTTATAATA
Found at i:3791534 original size:20 final size:20
Alignment explanation
Indices: 3791497--3791553 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
3791487 AATATTTAAA
3791497 AATATTTTAAT-A-TTTTAT
1 AATATTTTAATAATTTTTAT
3791515 AATATTTTAATAATTTTTAT
1 AATATTTTAATAATTTTTAT
**
3791535 -ATAGTTTTTTTAATTTTTA
1 AATA-TTTTAATAATTTTTA
3791554 AAAATTTATT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 11 0.32
19 4 0.12
20 19 0.56
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (20 bp):
AATATTTTAATAATTTTTAT
Found at i:3791542 original size:11 final size:10
Alignment explanation
Indices: 3791486--3791560 Score: 50
Period size: 10 Copynumber: 7.6 Consensus size: 10
3791476 AATTTTTTTT
*
3791486 TAATATTTAA
1 TAATTTTTAA
*
3791496 AAATATTTTAA
1 TAAT-TTTTAA
3791507 T-A-TTTT-A
1 TAATTTTTAA
3791514 TAATATTTTAA
1 TAAT-TTTTAA
3791525 TAATTTTTATA
1 TAATTTTTA-A
* *
3791536 TAGTTTTT-T
1 TAATTTTTAA
3791545 TAATTTTTAA
1 TAATTTTTAA
*
3791555 AAATTT
1 TAATTT
3791561 ATTTATTTTT
Statistics
Matches: 50, Mismatches: 8, Indels: 14
0.69 0.11 0.19
Matches are distributed among these distances:
7 2 0.04
8 5 0.10
9 7 0.14
10 18 0.36
11 18 0.36
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (10 bp):
TAATTTTTAA
Done.