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 140 of 198
Found at i:44593347 original size:72 final size:72
Alignment explanation
Indices: 44593155--44593321 Score: 230
Period size: 72 Copynumber: 2.3 Consensus size: 72
44593145 AAAATCATAT
* * * *
44593155 ATAAACAACTATTGATAAAACTA-ATTTA-ATAAAAATAAGTAGAACATAAATTCAATATTTAAA
1 ATAAACAACTATTAATAAAACTAGA-TTACACATAAATAAGTAGAACATAAATTCAATATTCAAA
*
44593218 GACCAAAC
65 AACCAAAC
* *
44593226 ATAAACAACTATTAATAGAAGTAGATTACACATAAATAAGTAGAACATAAATTCAATATTCAAAA
1 ATAAACAACTATTAATAAAACTAGATTACACATAAATAAGTAGAACATAAATTCAATATTCAAAA
44593291 ACCAAAC
66 ACCAAAC
* *
44593298 ATAAATAACTATTGATAAAACTAG
1 ATAAACAACTATTAATAAAACTAG
44593322 TTTAGCATTG
Statistics
Matches: 83, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
71 23 0.28
72 60 0.72
ACGTcount: A:0.56, C:0.12, G:0.07, T:0.26
Consensus pattern (72 bp):
ATAAACAACTATTAATAAAACTAGATTACACATAAATAAGTAGAACATAAATTCAATATTCAAAA
ACCAAAC
Found at i:44593767 original size:18 final size:18
Alignment explanation
Indices: 44593746--44593811 Score: 114
Period size: 18 Copynumber: 3.7 Consensus size: 18
44593736 TCCATCAATT
*
44593746 TGAACATCATTTGAGATG
1 TGAACATCATTTGAAATG
44593764 TGAACATCATTTGAAATG
1 TGAACATCATTTGAAATG
*
44593782 TGAACATCATTTAAAATG
1 TGAACATCATTTGAAATG
44593800 TGAACATCATTT
1 TGAACATCATTT
44593812 CTCATATTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 46 1.00
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (18 bp):
TGAACATCATTTGAAATG
Found at i:44599609 original size:7 final size:7
Alignment explanation
Indices: 44599597--44599657 Score: 61
Period size: 7 Copynumber: 8.7 Consensus size: 7
44599587 GAATTTTTTG
44599597 TTATTAA
1 TTATTAA
44599604 TTATTAA
1 TTATTAA
*
44599611 TTATAAA
1 TTATTAA
*
44599618 TTATTTA
1 TTATTAA
**
44599625 TGT-TTTG
1 T-TATTAA
44599632 TTATTAA
1 TTATTAA
44599639 TTATTAA
1 TTATTAA
*
44599646 TTATAAA
1 TTATTAA
44599653 TTATT
1 TTATT
44599658 TATGTTTAGT
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
6 1 0.02
7 42 0.95
8 1 0.02
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (7 bp):
TTATTAA
Found at i:44599633 original size:35 final size:35
Alignment explanation
Indices: 44599592--44599664 Score: 146
Period size: 35 Copynumber: 2.1 Consensus size: 35
44599582 ATTGTGAATT
44599592 TTTTGTTATTAATTATTAATTATAAATTATTTATG
1 TTTTGTTATTAATTATTAATTATAAATTATTTATG
44599627 TTTTGTTATTAATTATTAATTATAAATTATTTATG
1 TTTTGTTATTAATTATTAATTATAAATTATTTATG
44599662 TTT
1 TTT
44599665 AGTGTTTATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (35 bp):
TTTTGTTATTAATTATTAATTATAAATTATTTATG
Found at i:44599713 original size:21 final size:21
Alignment explanation
Indices: 44599688--44599832 Score: 124
Period size: 21 Copynumber: 7.1 Consensus size: 21
44599678 TGGATTAGTA
44599688 TTTTGTATGAATATTGTAATT
1 TTTTGTATGAATATTGTAATT
*
44599709 TTTTGGATGAATATTGTAA--
1 TTTTGTATGAATATTGTAATT
44599728 TTTTGTATGAATATTGTAATT
1 TTTTGTATGAATATTGTAATT
* * *
44599749 ATTTTATAATTAATTTTGT-ATT
1 -TTTTGT-ATGAATATTGTAATT
* * * ** *
44599771 TATAGTTTTGGGT-TAGT-A--
1 TTTTG-TATGAATATTGTAATT
44599789 TTTTGTATGAATATTGTAATT
1 TTTTGTATGAATATTGTAATT
44599810 TTTTGTATGAATATTGTAATT
1 TTTTGTATGAATATTGTAATT
44599831 TT
1 TT
44599833 GTAATTTTGT
Statistics
Matches: 96, Mismatches: 19, Indels: 18
0.72 0.14 0.14
Matches are distributed among these distances:
17 4 0.04
18 6 0.06
19 19 0.20
20 4 0.04
21 45 0.47
22 9 0.09
23 9 0.09
ACGTcount: A:0.28, C:0.00, G:0.15, T:0.57
Consensus pattern (21 bp):
TTTTGTATGAATATTGTAATT
Found at i:44599748 original size:101 final size:101
Alignment explanation
Indices: 44599643--44599835 Score: 291
Period size: 101 Copynumber: 1.9 Consensus size: 101
44599633 TATTAATTAT
* * *
44599643 TAATTA-TAAATTATTTATGTTTAGTGTTTATAG-TTTGGATTAGTATTTTGTATGAATATTGTA
1 TAATTATTAAATAATTAAT-TTT-GTATTTATAGTTTTGGATTAGTATTTTGTATGAATATTGTA
44599706 ATTTTTTGGATGAATATTGTAATTTTGTATGAATATTG
64 ATTTTTTGGATGAATATTGTAATTTTGTATGAATATTG
** *
44599744 TAATTATTTTATAATTAATTTTGTATTTATAGTTTTGGGTTAGTATTTTGTATGAATATTGTAAT
1 TAATTATTAAATAATTAATTTTGTATTTATAGTTTTGGATTAGTATTTTGTATGAATATTGTAAT
*
44599809 TTTTTGTATGAATATTGTAATTTTGTA
66 TTTTTGGATGAATATTGTAATTTTGTA
44599836 ATTTTGTATG
Statistics
Matches: 83, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
100 9 0.11
101 66 0.80
102 8 0.10
ACGTcount: A:0.29, C:0.00, G:0.16, T:0.55
Consensus pattern (101 bp):
TAATTATTAAATAATTAATTTTGTATTTATAGTTTTGGATTAGTATTTTGTATGAATATTGTAAT
TTTTTGGATGAATATTGTAATTTTGTATGAATATTG
Found at i:44599832 original size:40 final size:40
Alignment explanation
Indices: 44599688--44599835 Score: 110
Period size: 40 Copynumber: 3.6 Consensus size: 40
44599678 TGGATTAGTA
*
44599688 TTTTGTATGAATATTGTAATTTTTTGGATGAATATTGTAA--
1 TTTTGTATGAATATTGTAA--TTTTGTATGAATATTGTAATT
*
44599728 TTTTGTATGAATATTGTAATTATTTTAT-AATTAATTTTGT-ATT
1 TTTTGTATGAATATTGTAATT-TTGTATGAA-T-A--TTGTAATT
* * * ** *
44599771 TATAGTTTTGGGT-TAGT-ATTTTGTATGAATATTGTAATT
1 TTTTG-TATGAATATTGTAATTTTGTATGAATATTGTAATT
44599810 TTTTGTATGAATATTGTAATTTTGTA
1 TTTTGTATGAATATTGTAATTTTGTA
44599836 ATTTTGTATG
Statistics
Matches: 81, Mismatches: 15, Indels: 24
0.68 0.12 0.20
Matches are distributed among these distances:
38 12 0.15
39 14 0.17
40 29 0.36
41 7 0.09
42 9 0.11
43 6 0.07
44 4 0.05
ACGTcount: A:0.28, C:0.00, G:0.16, T:0.56
Consensus pattern (40 bp):
TTTTGTATGAATATTGTAATTTTGTATGAATATTGTAATT
Found at i:44599835 original size:29 final size:29
Alignment explanation
Indices: 44599802--44599886 Score: 147
Period size: 27 Copynumber: 3.0 Consensus size: 29
44599792 TGTATGAATA
44599802 TTGTAATTTTTTGTATGAATATTGTAATT
1 TTGTAATTTTTTGTATGAATATTGTAATT
*
44599831 TTGTAA--TTTTGTATGAATATTGTAATA
1 TTGTAATTTTTTGTATGAATATTGTAATT
44599858 TTGTAATTTTTTGTATGAATATTGTAATT
1 TTGTAATTTTTTGTATGAATATTGTAATT
44599887 ATTTTATAAT
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
27 26 0.50
29 26 0.50
ACGTcount: A:0.29, C:0.00, G:0.14, T:0.56
Consensus pattern (29 bp):
TTGTAATTTTTTGTATGAATATTGTAATT
Found at i:44599883 original size:48 final size:49
Alignment explanation
Indices: 44599697--44599886 Score: 140
Period size: 48 Copynumber: 3.7 Consensus size: 49
44599687 ATTTTGTATG
*
44599697 AATATTGTAATTTTTTGGA-TGAATATTGTAATTTTGTATGAATATTGT
1 AATATTGTAATTTTTTGTATTGAATATTGTAATTTTGTATGAATATTGT
* * *
44599745 AATTATTTTATAATTAATTTTGTATTTATAGTTTTGGGTTAGTATTTTGTATGAATATTGT
1 AA-TA--TTGTAATT--TTTTGTATTGA-A-TATT--G-TA--ATTTTGTATGAATATTGT
* * *
44599806 AAT-TT-T--TTGTATGAATATTGTAATTTTGTAATTTTGTATGAATATTGT
1 AATATTGTAATTTTTTG--TATTG-AATATTGTAATTTTGTATGAATATTGT
44599854 AATATTGTAATTTTTTGTA-TGAATATTGTAATT
1 AATATTGTAATTTTTTGTATTGAATATTGTAATT
44599887 ATTTTATAAT
Statistics
Matches: 112, Mismatches: 10, Indels: 40
0.69 0.06 0.25
Matches are distributed among these distances:
48 34 0.30
49 6 0.05
50 5 0.04
51 8 0.07
52 8 0.07
53 10 0.09
54 9 0.08
55 2 0.02
56 4 0.04
57 2 0.02
58 1 0.01
59 2 0.02
60 1 0.01
61 20 0.18
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.55
Consensus pattern (49 bp):
AATATTGTAATTTTTTGTATTGAATATTGTAATTTTGTATGAATATTGT
Found at i:44599942 original size:59 final size:60
Alignment explanation
Indices: 44599879--44599999 Score: 174
Period size: 59 Copynumber: 2.0 Consensus size: 60
44599869 TGTATGAATA
* * * * *
44599879 TTGTAATTATTTTATAA-TTAATTTGTTAGTAATTTAGGATTATGTTATAAATT-TTGTGT
1 TTGTAATTA-TTTAAAATTTAATTTATTAGGAATTTAGGATTAAGCTATAAATTGTTGTGT
44599938 TTGTAATTATTTAAAATTTAATTTATTAGGAATTTAGGATTAAGCTATAAATTGTTGTGT
1 TTGTAATTATTTAAAATTTAATTTATTAGGAATTTAGGATTAAGCTATAAATTGTTGTGT
44599998 TT
1 TT
44600000 AGTTTAGTAT
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
58 6 0.11
59 41 0.75
60 8 0.15
ACGTcount: A:0.32, C:0.01, G:0.14, T:0.53
Consensus pattern (60 bp):
TTGTAATTATTTAAAATTTAATTTATTAGGAATTTAGGATTAAGCTATAAATTGTTGTGT
Found at i:44600141 original size:16 final size:15
Alignment explanation
Indices: 44600117--44600151 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
44600107 CTCATTTAAT
*
44600117 TTTTCTATAATGTAA
1 TTTTATATAATGTAA
44600132 CTTTTATATAATGTAA
1 -TTTTATATAATGTAA
44600148 TTTT
1 TTTT
44600152 GTTTGATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.57
Consensus pattern (15 bp):
TTTTATATAATGTAA
Found at i:44601969 original size:14 final size:15
Alignment explanation
Indices: 44601944--44601972 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
44601934 ATTTTATTTT
44601944 ATAATAAATTTTAAA
1 ATAATAAATTTTAAA
44601959 ATAAT-AATTTTAAA
1 ATAATAAATTTTAAA
44601973 GTTTAAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
ATAATAAATTTTAAA
Found at i:44602015 original size:18 final size:19
Alignment explanation
Indices: 44601992--44602029 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
44601982 ATATTCTTCA
*
44601992 TATATTATTAA-AAATATT
1 TATATTAGTAATAAATATT
44602010 TATATTAGTAATAAATATT
1 TATATTAGTAATAAATATT
44602029 T
1 T
44602030 TATAATATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (19 bp):
TATATTAGTAATAAATATT
Found at i:44610122 original size:2 final size:2
Alignment explanation
Indices: 44610115--44610151 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
44610105 TATACTTGTG
44610115 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
44610152 ATAGTGAGCC
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:44611122 original size:19 final size:19
Alignment explanation
Indices: 44611100--44611148 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
44611090 CTATCTTTTT
**
44611100 TTTTTTGTATTTTCTTTGA
1 TTTTTTGTATCATCTTTGA
*
44611119 TTTTTCTCT-TCATCTTTGA
1 TTTTT-TGTATCATCTTTGA
44611138 TTTTTTGTATC
1 TTTTTTGTATC
44611149 GGCACCCGGA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
18 2 0.08
19 20 0.83
20 2 0.08
ACGTcount: A:0.10, C:0.12, G:0.08, T:0.69
Consensus pattern (19 bp):
TTTTTTGTATCATCTTTGA
Found at i:44613263 original size:15 final size:15
Alignment explanation
Indices: 44613243--44613290 Score: 78
Period size: 15 Copynumber: 3.1 Consensus size: 15
44613233 TTGATCTTTC
44613243 TAGTATTATATATTA
1 TAGTATTATATATTA
44613258 TAGTATTATATATTTTA
1 TAGTATTATATA--TTA
44613275 TAGTATTATATATTA
1 TAGTATTATATATTA
44613290 T
1 T
44613291 GATTTTAGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
15 16 0.52
17 15 0.48
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (15 bp):
TAGTATTATATATTA
Found at i:44613275 original size:17 final size:17
Alignment explanation
Indices: 44613243--44613288 Score: 78
Period size: 17 Copynumber: 2.8 Consensus size: 17
44613233 TTGATCTTTC
44613243 TAGTATTATATA--TTA
1 TAGTATTATATATTTTA
44613258 TAGTATTATATATTTTA
1 TAGTATTATATATTTTA
44613275 TAGTATTATATATT
1 TAGTATTATATATT
44613289 ATGATTTTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.41
17 17 0.59
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.57
Consensus pattern (17 bp):
TAGTATTATATATTTTA
Found at i:44613350 original size:17 final size:17
Alignment explanation
Indices: 44613330--44613364 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
44613320 ATATTAAGAA
44613330 TTTTATTAAATTATATT
1 TTTTATTAAATTATATT
44613347 TTTTATTAAATTATATT
1 TTTTATTAAATTATATT
44613364 T
1 T
44613365 AAAAATAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTTATTAAATTATATT
Found at i:44613467 original size:18 final size:18
Alignment explanation
Indices: 44613433--44613483 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
44613423 CTAAGAATAT
*
44613433 TTAATATTA-ATAATTTTA
1 TTAA-ATTATATATTTTTA
44613451 TTAAATTATATATTTTTA
1 TTAAATTATATATTTTTA
*
44613469 CTAAATTATAT-TTTT
1 TTAAATTATATATTTT
44613484 AATAATTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
17 8 0.27
18 22 0.73
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (18 bp):
TTAAATTATATATTTTTA
Found at i:44613490 original size:15 final size:15
Alignment explanation
Indices: 44613459--44613510 Score: 56
Period size: 16 Copynumber: 3.5 Consensus size: 15
44613449 TATTAAATTA
*
44613459 TATATTTTTACTAAAT
1 TATATTTTTAAT-AAT
44613475 TATATTTTTAATAAT
1 TATATTTTTAATAAT
44613490 TAT-TATTTT-A-AAT
1 TATAT-TTTTAATAAT
44613503 TATATTTT
1 TATATTTT
44613511 ATAGTATTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
13 9 0.27
14 3 0.09
15 10 0.30
16 11 0.33
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (15 bp):
TATATTTTTAATAAT
Found at i:44613494 original size:18 final size:18
Alignment explanation
Indices: 44613454--44613495 Score: 54
Period size: 16 Copynumber: 2.5 Consensus size: 18
44613444 AATTTTATTA
*
44613454 AATTA-TATATTTTTACT
1 AATTATTATATTTTTAAT
44613471 AA--ATTATATTTTTAAT
1 AATTATTATATTTTTAAT
44613487 AATTATTAT
1 AATTATTAT
44613496 TTTAAATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
15 1 0.05
16 13 0.62
17 2 0.10
18 5 0.24
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (18 bp):
AATTATTATATTTTTAAT
Found at i:44613519 original size:28 final size:29
Alignment explanation
Indices: 44613470--44613525 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
44613460 ATATTTTTAC
44613470 TAAATTATATTTTTAATAATTAT-TATTT
1 TAAATTATATTTTTAATAATTATATATTT
*
44613498 TAAATTATATTTTATAGT-ATTATATATT
1 TAAATTATATTTT-TAATAATTATATATT
44613526 ATGATTTTAG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 18 0.72
29 7 0.28
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (29 bp):
TAAATTATATTTTTAATAATTATATATTT
Found at i:44613589 original size:18 final size:18
Alignment explanation
Indices: 44613568--44613721 Score: 76
Period size: 18 Copynumber: 8.9 Consensus size: 18
44613558 ATATTAAGAA
44613568 TTTTATTAAATTATATAT
1 TTTTATTAAATTATATAT
44613586 TTTTATTAAA-T-TATA-
1 TTTTATTAAATTATATAT
* *
44613601 -TTTAAT-AATAAT-TAT
1 TTTTATTAAATTATATAT
* * *
44613616 TTTAAATTATATTATATAG
1 TTT-TATTAAATTATATAT
* * *
44613635 TATTA-TATATTAT-GA-
1 TTTTATTAAATTATATAT
*
44613650 TTTTATTAAATTCATATAA
1 TTTTATTAAATT-ATATAT
*** * *
44613669 GAATATTTAATATTA-AGAA
1 TTTTA-TTAA-ATTATATAT
44613688 TTTTATTAAATTATATAT
1 TTTTATTAAATTATATAT
44613706 TTTTATTAAATTATAT
1 TTTTATTAAATTATAT
44613722 TTAATAATAA
Statistics
Matches: 100, Mismatches: 22, Indels: 28
0.67 0.15 0.19
Matches are distributed among these distances:
13 2 0.02
14 7 0.07
15 5 0.05
16 12 0.12
17 17 0.17
18 38 0.38
19 11 0.11
20 5 0.05
21 3 0.03
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.55
Consensus pattern (18 bp):
TTTTATTAAATTATATAT
Found at i:44613660 original size:120 final size:120
Alignment explanation
Indices: 44613266--44613863 Score: 1017
Period size: 122 Copynumber: 5.0 Consensus size: 120
44613256 TATAGTATTA
44613266 TATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAAT-TTTAATATTAAGAA
1 TATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAA
* *
44613330 TTTTATTAAATTATAT-TTTTTATTAAATTATATTTAAAAATAATTAATTTAAAT
66 TTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAAT
* *
44613384 TATATTTTATAGTATTGTATATTATGATTTTAGTAAATTC---TAAGAATATTTAATATTAATAA
1 TATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAA
* *
44613446 TTTTATTAAATTATATATTTTTACTAAATTATATTTTTAATAATTATTATTTTAAAT
66 TTTTATTAAATTATATATTTTTATTAAATTATA--TTTAATAATAATTATTTTAAAT
*
44613503 TATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATTTAAGAATATTTAATATTAAGAA
1 TATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAA
44613568 TTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAAT
66 TTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAAT
* *
44613623 TATATTATATAGTATTATATATTATGATTTTATTAAATTCATATAAGAATATTTAATATTAAGAA
1 TATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAA
*
44613688 TTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAAT
66 TTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAAT
*
44613743 TATATTTTATAGTATTATATATATTATGATTTTAGAAAATTCATATAAGAATATTTAATATTAAG
1 TATATTTTATAGTA-T-TATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAG
*
44613808 AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAA
64 AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAA
44613864 ATATGATTAA
Statistics
Matches: 454, Mismatches: 17, Indels: 14
0.94 0.04 0.03
Matches are distributed among these distances:
115 7 0.02
116 29 0.06
117 15 0.03
118 39 0.09
119 58 0.13
120 150 0.33
121 1 0.00
122 155 0.34
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.52
Consensus pattern (120 bp):
TATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAA
TTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAAT
Found at i:44613776 original size:242 final size:238
Alignment explanation
Indices: 44613266--44613872 Score: 1013
Period size: 242 Copynumber: 2.5 Consensus size: 238
44613256 TATAGTATTA
44613266 TATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAAT-TTTAATATTAAGAA
1 TATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAA
* * *
44613330 TTTTATTAAATTATAT-TTTTTATTAAATTATATTTAAAAATAATTAATTTAAATTATATTTTAT
66 TTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTATAT
* *
44613394 AGTATTGTATATTATGATTTTAGTAAATTCTAAGAATATTTAATATTAATAATTTTATTAAATTA
131 AGTATTATATATTATGATTTTAGTAAATTCTAAGAATATTTAATATTAAGAATTTTATTAAATTA
* *
44613459 TATATTTTTACTAAATTATATTTTTAATAATTATTATTTTAAAT
196 TATATTTTTACTAAATTATA-TTTTAATAATAATTATGTTAAAT
*
44613503 TATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATTTAAGAATATTTAATATTAAGAA
1 TATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAA
44613568 TTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTATAT
66 TTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTATAT
*
44613633 AGTATTATATATTATGATTTTATTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAA
131 AGTATTATATATTATGATTTTAGTAAATTC---TAAGAATATTTAATATTAAGAATTTTATTAAA
*
44613698 TTATATATTTTTATTAAATTATA-TTTAATAATAATTATGTTAAAT
193 TTATATATTTTTACTAAATTATATTTTAATAATAATTATGTTAAAT
*
44613743 TATATTTTATAGTATTATATATATTATGATTTTAGAAAATTCATATAAGAATATTTAATATTAAG
1 TATATTTTATAGTA-T-TATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAG
* *
44613808 AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAAATATGATTA
64 AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTAT-ATTA
44613873 AATTATTTAT
Statistics
Matches: 348, Mismatches: 14, Indels: 10
0.94 0.04 0.03
Matches are distributed among these distances:
237 49 0.14
238 30 0.09
239 73 0.21
240 34 0.10
241 1 0.00
242 157 0.45
243 4 0.01
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.52
Consensus pattern (238 bp):
TATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAA
TTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTATAT
AGTATTATATATTATGATTTTAGTAAATTCTAAGAATATTTAATATTAAGAATTTTATTAAATTA
TATATTTTTACTAAATTATATTTTAATAATAATTATGTTAAAT
Found at i:44614058 original size:44 final size:45
Alignment explanation
Indices: 44614008--44614097 Score: 148
Period size: 45 Copynumber: 2.0 Consensus size: 45
44613998 ACATCGTTCT
44614008 ATTCAACCAAACACA-AGAA-TACTATTACGCCTCTATTCCATTAC
1 ATTCAACCAAACA-ATAGAATTACTATTACGCCTCTATTCCATTAC
*
44614052 ATTCAACCAAACAATTGAATTACTATTACGCCTCTATTCCATTAC
1 ATTCAACCAAACAATAGAATTACTATTACGCCTCTATTCCATTAC
44614097 A
1 A
44614098 CCTCTATTTC
Statistics
Matches: 43, Mismatches: 1, Indels: 3
0.91 0.02 0.06
Matches are distributed among these distances:
43 1 0.02
44 16 0.37
45 26 0.60
ACGTcount: A:0.38, C:0.28, G:0.04, T:0.30
Consensus pattern (45 bp):
ATTCAACCAAACAATAGAATTACTATTACGCCTCTATTCCATTAC
Found at i:44614101 original size:16 final size:16
Alignment explanation
Indices: 44614076--44614113 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
44614066 TTGAATTACT
*
44614076 ATTACGCCTCTATTCC
1 ATTACACCTCTATTCC
*
44614092 ATTACACCTCTATTTC
1 ATTACACCTCTATTCC
44614108 ATTACA
1 ATTACA
44614114 ACGAACTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.26, C:0.32, G:0.03, T:0.39
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:44626399 original size:22 final size:21
Alignment explanation
Indices: 44626352--44626404 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 21
44626342 TTTAGTTTTT
*
44626352 TTAATGTTTTAACCTTTAATA
1 TTAATATTTTAACCTTTAATA
* * *
44626373 ATAATATTTTAACATTTTATTA
1 TTAATATTTTAAC-CTTTAATA
44626395 TTAATTATTT
1 TTAA-TATTT
44626405 AATTAAAATT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
21 11 0.44
22 9 0.36
23 5 0.20
ACGTcount: A:0.36, C:0.06, G:0.02, T:0.57
Consensus pattern (21 bp):
TTAATATTTTAACCTTTAATA
Found at i:44630405 original size:26 final size:26
Alignment explanation
Indices: 44630367--44630427 Score: 97
Period size: 26 Copynumber: 2.3 Consensus size: 26
44630357 TATTTAAGCA
*
44630367 TATATCACTACACATATAAATCCTAT
1 TATATCACAACACATATAAATCCTAT
44630393 TATATCACAACACATATAAATCCTAT
1 TATATCACAACACATATAAATCCTAT
44630419 T-TAATCACA
1 TAT-ATCACA
44630428 TTTAGTCACA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
25 1 0.03
26 32 0.97
ACGTcount: A:0.44, C:0.23, G:0.00, T:0.33
Consensus pattern (26 bp):
TATATCACAACACATATAAATCCTAT
Found at i:44630878 original size:35 final size:36
Alignment explanation
Indices: 44630830--44630911 Score: 114
Period size: 36 Copynumber: 2.3 Consensus size: 36
44630820 TACATTATAA
*
44630830 TCACTATTACATGG-TATGAA-AACATACCCACATAT
1 TCACTATCACATGGCT-TGAATAACATACCCACATAT
*
44630865 TTACTATCACATGGCTTGAATAACATACCCACATAT
1 TCACTATCACATGGCTTGAATAACATACCCACATAT
*
44630901 TCACTTTCACA
1 TCACTATCACA
44630912 ACAATCATCA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
35 16 0.39
36 25 0.61
ACGTcount: A:0.37, C:0.26, G:0.07, T:0.30
Consensus pattern (36 bp):
TCACTATCACATGGCTTGAATAACATACCCACATAT
Found at i:44634987 original size:17 final size:17
Alignment explanation
Indices: 44634967--44635004 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
44634957 TGAAACATTA
44634967 AAGTTAATTGAACATAG
1 AAGTTAATTGAACATAG
*
44634984 AAGTTAATTGGACATAG
1 AAGTTAATTGAACATAG
44635001 AAGT
1 AAGT
44635005 ATGCTAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.45, C:0.05, G:0.21, T:0.29
Consensus pattern (17 bp):
AAGTTAATTGAACATAG
Found at i:44640898 original size:131 final size:131
Alignment explanation
Indices: 44640659--44641247 Score: 919
Period size: 131 Copynumber: 4.5 Consensus size: 131
44640649 AAATCAGTAA
* *
44640659 AAATTGCAGATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCGAAGATGGCGAATCTTATTGTCC
1 AAATGGCAGATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCGAAGATGGCGAATCTTATCGTCC
* * *
44640724 CCAGGAGTAGGGAAATAGATTTAAGTCACAAGTCCTATGTCCCTAACCAGCAGTGGAATAGGTTG
66 CCAGGAGTAGGGAAACAGATTTAAGCCACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTG
44640789 G
131 G
** *
44640790 AAATGGCAGATCTTATCTCCCTAAGCAGTAGAAGAGTAGATCGAAGATGGCGAATCTTATCGTCC
1 AAATGGCAGATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCGAAGATGGCGAATCTTATCGTCC
*
44640855 CCAGGAGTAGGGAAACAGATTTAAGCCACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTA
66 CCAGGAGTAGGGAAACAGATTTAAGCCACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTG
44640920 G
131 G
* * *
44640921 AAATGGCAGATCTTATCTCCCTAAGAAGTAGCGGAGCAAATCGAAGATGGTGAATCTTATCGTCC
1 AAATGGCAGATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCGAAGATGGCGAATCTTATCGTCC
44640986 CCAGGAGTAGGGAAACAGATTTAAGCCACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTG
66 CCAGGAGTAGGGAAACAGATTTAAGCCACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTG
44641051 G
131 G
* * * *
44641052 AAATGGCAGATCTTACCTCCCTGAGCAGTAGCGAAGCAGATCGAAGATGGCGAATCTTATCTTCC
1 AAATGGCAGATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCGAAGATGGCGAATCTTATCGTCC
* * * *
44641117 CCAGGAGTAGGGAAACAGATTTAAGCCACAAGTCCTGTGACCCTGACCAGTAGTGGGATAGGTTG
66 CCAGGAGTAGGGAAACAGATTTAAGCCACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTG
44641182 G
131 G
* * * * * * * *
44641183 AAATTGTAGATCTTGTCTCCTTAAGCAGTAGCGGAGTAGATCGAATACGGCGAATCTGATC-TCC
1 AAATGGCAGATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCGAAGATGGCGAATCTTATCGTCC
44641247 C
66 C
44641248 TGAGATTACA
Statistics
Matches: 420, Mismatches: 38, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
130 4 0.01
131 416 0.99
ACGTcount: A:0.30, C:0.21, G:0.26, T:0.23
Consensus pattern (131 bp):
AAATGGCAGATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCGAAGATGGCGAATCTTATCGTCC
CCAGGAGTAGGGAAACAGATTTAAGCCACAAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTG
G
Found at i:44645298 original size:22 final size:21
Alignment explanation
Indices: 44645252--44645298 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
44645242 ATGACATTCT
*
44645252 AAATTATACTTTTAAAAGAAT
1 AAATTATACTTTTAAAAGAAA
*
44645273 AAATTATTCTTATTAAATA-AAA
1 AAATTATACTT-TTAAA-AGAAA
44645295 AAAT
1 AAAT
44645299 GTCTCAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 10 0.45
22 11 0.50
23 1 0.05
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.38
Consensus pattern (21 bp):
AAATTATACTTTTAAAAGAAA
Found at i:44645603 original size:2 final size:2
Alignment explanation
Indices: 44645596--44645635 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
44645586 TTATCTTCAA
44645596 AT AT AT AT AT 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 AT AT AT AT AT
44645636 TGTTAAACTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:44645734 original size:18 final size:17
Alignment explanation
Indices: 44645713--44645746 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
44645703 AATAAAAAAA
44645713 TTATTATAGAAATTTAAT
1 TTATTA-AGAAATTTAAT
*
44645731 TTATTAATAAATTTAA
1 TTATTAAGAAATTTAA
44645747 AATAAGTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (17 bp):
TTATTAAGAAATTTAAT
Found at i:44648603 original size:49 final size:50
Alignment explanation
Indices: 44648511--44648608 Score: 153
Period size: 49 Copynumber: 2.0 Consensus size: 50
44648501 ATTTATTTAT
* * * *
44648511 AGGTTGAAAAAACCTTATTCTAATCAATGTCAAATAGATGAAGTGTAGTC
1 AGGTTGAAAAAACCTTATTCTAATCAATGTAAAATAAAAGAAGTATAGTC
44648561 AGGTTG-AAAAACCTTATTCTAATCAATGTAAAATAAAAGAAGTATAGT
1 AGGTTGAAAAAACCTTATTCTAATCAATGTAAAATAAAAGAAGTATAGT
44648609 TCTATATGGA
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
49 38 0.86
50 6 0.14
ACGTcount: A:0.44, C:0.10, G:0.16, T:0.30
Consensus pattern (50 bp):
AGGTTGAAAAAACCTTATTCTAATCAATGTAAAATAAAAGAAGTATAGTC
Found at i:44662853 original size:3 final size:3
Alignment explanation
Indices: 44662845--44662870 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
44662835 TTATGTAAAA
44662845 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
44662871 AGAAAGAAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:44664094 original size:18 final size:19
Alignment explanation
Indices: 44664059--44664095 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
44664049 GTTAAAAGGT
44664059 TTTTTTGATGCATTTTATA
1 TTTTTTGATGCATTTTATA
44664078 TTTTTT-ATG-ATTATTATA
1 TTTTTTGATGCATT-TTATA
44664096 AAATTCTACA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
17 3 0.18
18 8 0.47
19 6 0.35
ACGTcount: A:0.24, C:0.03, G:0.08, T:0.65
Consensus pattern (19 bp):
TTTTTTGATGCATTTTATA
Found at i:44664148 original size:19 final size:20
Alignment explanation
Indices: 44664104--44664157 Score: 67
Period size: 19 Copynumber: 2.6 Consensus size: 20
44664094 TAAAATTCTA
44664104 CAATATTTTATAAATTTTTTT
1 CAAT-TTTTATAAATTTTTTT
44664125 CAATTTTTAT-AA-TTTTTT
1 CAATTTTTATAAATTTTTTT
44664143 CTAATTTTTAATAAA
1 C-AATTTTT-ATAAA
44664158 ACTTAAATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
18 7 0.23
19 9 0.30
20 8 0.27
21 6 0.20
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (20 bp):
CAATTTTTATAAATTTTTTT
Found at i:44664194 original size:28 final size:29
Alignment explanation
Indices: 44664134--44664209 Score: 75
Period size: 29 Copynumber: 2.6 Consensus size: 29
44664124 TCAATTTTTA
* *
44664134 TAAT-TTTTTCTAATTTTTAATAAAACTT
1 TAATATTTTTATATTTTTTAATAAAACTT
* *
44664162 AAATATTTTTATATTTTTTATTAAAA-TT
1 TAATATTTTTATATTTTTTAATAAAACTT
*
44664190 TAATAATTTATATGATTTTT
1 TAAT-ATTTTTAT-ATTTTT
44664210 ATTTTTTATA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
28 8 0.21
29 25 0.64
30 6 0.15
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.59
Consensus pattern (29 bp):
TAATATTTTTATATTTTTTAATAAAACTT
Found at i:44664224 original size:9 final size:9
Alignment explanation
Indices: 44664071--44664225 Score: 62
Period size: 9 Copynumber: 16.4 Consensus size: 9
44664061 TTTTGATGCA
*
44664071 TTTTATATT
1 TTTTATAAT
*
44664080 TTTTATGAT
1 TTTTATAAT
* *
44664089 TATTATAAAA
1 TTTTAT-AAT
* *
44664099 TTCTACAAT
1 TTTTATAAT
44664108 ATTTTATAAAT
1 -TTTTAT-AAT
*
44664119 TTTTTTCAAT
1 TTTTAT-AAT
44664129 TTTTATAATT
1 TTTTATAA-T
*
44664139 TTTTCTAAT
1 TTTTATAAT
*
44664148 TTTTAATAAA
1 TTTT-ATAAT
** *
44664158 ACTTAAATAT
1 TTTTATA-AT
*
44664168 TTTTATATT
1 TTTTATAAT
*
44664177 TTTTATTAAAA
1 TTTTA-T-AAT
*
44664188 TTTAATAAT
1 TTTTATAAT
* *
44664197 TTATATGAT
1 TTTTATAAT
44664206 TTTTAT--T
1 TTTTATAAT
44664213 TTTTATAAT
1 TTTTATAAT
44664222 TTTT
1 TTTT
44664226 TGCCACATGT
Statistics
Matches: 103, Mismatches: 33, Indels: 20
0.66 0.21 0.13
Matches are distributed among these distances:
7 7 0.07
9 47 0.46
10 41 0.40
11 8 0.08
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.61
Consensus pattern (9 bp):
TTTTATAAT
Found at i:44664965 original size:3 final size:3
Alignment explanation
Indices: 44664957--44664988 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
44664947 TTGACCAAGT
44664957 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
44664989 TAATTTTGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.34, G:0.00, T:0.34
Consensus pattern (3 bp):
TCA
Found at i:44665681 original size:16 final size:16
Alignment explanation
Indices: 44665660--44665693 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
44665650 TCATAACGGT
44665660 TACCCCTCCCAACAGC
1 TACCCCTCCCAACAGC
*
44665676 TACCCCTCCCAACGGC
1 TACCCCTCCCAACAGC
44665692 TA
1 TA
44665694 TTTAAATAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.53, G:0.09, T:0.15
Consensus pattern (16 bp):
TACCCCTCCCAACAGC
Found at i:44667413 original size:17 final size:16
Alignment explanation
Indices: 44667393--44667441 Score: 64
Period size: 17 Copynumber: 3.0 Consensus size: 16
44667383 AAAAAAAAAA
44667393 CTAAACCCTATAAAACC
1 CTAAA-CCTATAAAACC
*
44667410 CTAAA-CTATAAAACA
1 CTAAACCTATAAAACC
44667425 CTAAAACCTATAAAACC
1 CT-AAACCTATAAAACC
44667442 TTAATCCTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 11 0.39
16 3 0.11
17 14 0.50
ACGTcount: A:0.53, C:0.29, G:0.00, T:0.18
Consensus pattern (16 bp):
CTAAACCTATAAAACC
Found at i:44668330 original size:26 final size:23
Alignment explanation
Indices: 44668288--44668347 Score: 59
Period size: 26 Copynumber: 2.5 Consensus size: 23
44668278 TTTGGTTCTC
*
44668288 GATTTTTATATTGATTTTGGAATAT
1 GATTTTTAGATTGATTTT--AATAT
44668313 AGATTTTTAGACTT-ATTTTAATAT
1 -GATTTTTAGA-TTGATTTTAATAT
*
44668337 GACTTTTAGAT
1 GATTTTTAGAT
44668348 ATTATTTGGT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
22 1 0.03
23 9 0.29
24 5 0.16
26 14 0.45
27 2 0.06
ACGTcount: A:0.30, C:0.03, G:0.13, T:0.53
Consensus pattern (23 bp):
GATTTTTAGATTGATTTTAATAT
Found at i:44668352 original size:24 final size:24
Alignment explanation
Indices: 44668308--44668354 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
44668298 TTGATTTTGG
* *
44668308 AATATAGATTTTTAGACTTATTTT
1 AATATAGACTTTTAGAATTATTTT
44668332 AATAT-GACTTTTAGATATTATTT
1 AATATAGACTTTTAGA-ATTATTT
44668355 GGTAAAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.34, C:0.04, G:0.09, T:0.53
Consensus pattern (24 bp):
AATATAGACTTTTAGAATTATTTT
Found at i:44669501 original size:20 final size:22
Alignment explanation
Indices: 44669464--44669503 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
44669454 ATATAAACAC
*
44669464 ATATAATATAATTTTTATAAAT
1 ATATAATATAATTATTATAAAT
44669486 ATATAA-ATAA-TATTATAA
1 ATATAATATAATTATTATAA
44669504 TGTGTACTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 4 0.24
22 6 0.35
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
ATATAATATAATTATTATAAAT
Found at i:44674013 original size:49 final size:49
Alignment explanation
Indices: 44673904--44674013 Score: 139
Period size: 49 Copynumber: 2.2 Consensus size: 49
44673894 GAAACCATTG
* *
44673904 TTGTCGGACAACCCAGGGTGGTAGAATGTACATATGCTAGTAGTCATCA
1 TTGTCGGGCAACCCAGGGTGATAGAATGTACATATGCTAGTAGTCATCA
** * * * * *
44673953 TTACCGAGCAACCCAGGGTGATAGTATGTACATGTTCTATTAGTCATCA
1 TTGTCGGGCAACCCAGGGTGATAGAATGTACATATGCTAGTAGTCATCA
44674002 TTGTCGGGCAAC
1 TTGTCGGGCAAC
44674014 TTGGGATGAC
Statistics
Matches: 49, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.28
Consensus pattern (49 bp):
TTGTCGGGCAACCCAGGGTGATAGAATGTACATATGCTAGTAGTCATCA
Found at i:44679454 original size:136 final size:136
Alignment explanation
Indices: 44679210--44679465 Score: 476
Period size: 136 Copynumber: 1.9 Consensus size: 136
44679200 TGAGTGATAA
*
44679210 AACTCAGTGGTATTTTTATAATTCAATATAATGTAAATGTTATTCAAATGCAAATAATCAATTCA
1 AACTCAGTGGTATTTTTATAATTCAATATAATGTAAATATTATTCAAATGCAAATAATCAATTCA
* *
44679275 AATATATTTTTCAACTGATTAGTGCACCAAATTTTAACATAGACTTAGTAATCAATTCATTTGGT
66 AATATATTTTTCAACTAATTAGTACACCAAATTTTAACATAGACTTAGTAATCAATTCATTTGGT
44679340 TATTTC
131 TATTTC
44679346 AACTCAGTGGTATTTTTATAATTCAATATAATGTAAATATTATTCAAATGCAAATAATCAATTCA
1 AACTCAGTGGTATTTTTATAATTCAATATAATGTAAATATTATTCAAATGCAAATAATCAATTCA
*
44679411 AATATATTTTTCAACTAATTAGTATACCAAATTTTAACATAGACTTAGTAATCAA
66 AATATATTTTTCAACTAATTAGTACACCAAATTTTAACATAGACTTAGTAATCAA
44679466 CACCTACCTA
Statistics
Matches: 116, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
136 116 1.00
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.39
Consensus pattern (136 bp):
AACTCAGTGGTATTTTTATAATTCAATATAATGTAAATATTATTCAAATGCAAATAATCAATTCA
AATATATTTTTCAACTAATTAGTACACCAAATTTTAACATAGACTTAGTAATCAATTCATTTGGT
TATTTC
Found at i:44680165 original size:86 final size:86
Alignment explanation
Indices: 44680020--44680180 Score: 232
Period size: 86 Copynumber: 1.9 Consensus size: 86
44680010 AGCACTATAA
* * * *
44680020 TGCATCATCAGATAAATCGAAGGAAATATAATGGCATACACAGTTCATCATCGGACAAGCCGAAA
1 TGCATCATCAGATAAACCAAAGAAAATATAATGGCATACACAGTGCATCATCGGACAAGCCGAAA
*
44680085 CAATTGTACTGGCACGCGTAG
66 CAATTATACTGGCACGCGTAG
* * * *
44680106 TGCATCATCGGATAAACCAAAGAAAATATACTGGTATACATAGTGCATCATCGGACAAGCCGAAA
1 TGCATCATCAGATAAACCAAAGAAAATATAATGGCATACACAGTGCATCATCGGACAAGCCGAAA
*
44680171 TAATTATACT
66 CAATTATACT
44680181 AACACACATA
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
86 65 1.00
ACGTcount: A:0.39, C:0.20, G:0.19, T:0.22
Consensus pattern (86 bp):
TGCATCATCAGATAAACCAAAGAAAATATAATGGCATACACAGTGCATCATCGGACAAGCCGAAA
CAATTATACTGGCACGCGTAG
Found at i:44680193 original size:86 final size:86
Alignment explanation
Indices: 44680020--44680201 Score: 229
Period size: 86 Copynumber: 2.1 Consensus size: 86
44680010 AGCACTATAA
* * * * *
44680020 TGCATCATCAGATAAATCGAAGGAAATATAATGGCATACACAGTTCATCATCGGACAAGCCGAAA
1 TGCATCATCGGATAAACCAAAGAAAATATAATGGCATACACAGTGCATCATCGGACAAGCCGAAA
* ** * *
44680085 CAATTGTACTGGCACGCGTAG
66 CAATTATACTAACACACATAG
* * *
44680106 TGCATCATCGGATAAACCAAAGAAAATATACTGGTATACATAGTGCATCATCGGACAAGCCGAAA
1 TGCATCATCGGATAAACCAAAGAAAATATAATGGCATACACAGTGCATCATCGGACAAGCCGAAA
*
44680171 TAATTATACTAACACACATAG
66 CAATTATACTAACACACATAG
*
44680192 TGCATTATCG
1 TGCATCATCG
44680202 AAAAAATTGA
Statistics
Matches: 81, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
86 81 1.00
ACGTcount: A:0.39, C:0.20, G:0.18, T:0.23
Consensus pattern (86 bp):
TGCATCATCGGATAAACCAAAGAAAATATAATGGCATACACAGTGCATCATCGGACAAGCCGAAA
CAATTATACTAACACACATAG
Found at i:44680222 original size:86 final size:86
Alignment explanation
Indices: 44680043--44680266 Score: 223
Period size: 86 Copynumber: 2.6 Consensus size: 86
44680033 AAATCGAAGG
* * * * ** * *
44680043 AAATATAATGGCATACACAGTTCATCATCGGACAAGCCGAAACAATTGTACTGGCACGCGTAGTG
1 AAATATACTGGCATACACAGTGCATCATCGGACAAGCCGAAATAATTATACTAACACACATAGTG
* *
44680108 CATCATCGGATAAACCAAAGA
66 CATCATCGAAAAAACCAAAGA
* *
44680129 AAATATACTGGTATACATAGTGCATCATCGGACAAGCCGAAATAATTATACTAACACACATAGTG
1 AAATATACTGGCATACACAGTGCATCATCGGACAAGCCGAAATAATTATACTAACACACATAGTG
* *** **
44680194 CATTATCGAAAAAATTGAATT
66 CATCATCGAAAAAACCAAAGA
* * ** * * *
44680215 AATTATACTAGCACCCACAGTGCATCATCGAACAAGTCGAAGTAATTATACT
1 AAATATACTGGCATACACAGTGCATCATCGGACAAGCCGAAATAATTATACT
44680267 GGCACACAGA
Statistics
Matches: 111, Mismatches: 27, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
86 111 1.00
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.24
Consensus pattern (86 bp):
AAATATACTGGCATACACAGTGCATCATCGGACAAGCCGAAATAATTATACTAACACACATAGTG
CATCATCGAAAAAACCAAAGA
Found at i:44680299 original size:43 final size:43
Alignment explanation
Indices: 44680020--44680301 Score: 186
Period size: 43 Copynumber: 6.6 Consensus size: 43
44680010 AGCACTATAA
* * * * * * *
44680020 TGCATCATCAGATAAATCGAAGGAAATATAATGGCATACACAG
1 TGCATCATCGGACAAACCGAAGTAATTATACTGGCACACACAG
* * ** * * **
44680063 TTCATCATCGGACAAGCCGAAACAATTGTACTGGCACGCGTAG
1 TGCATCATCGGACAAACCGAAGTAATTATACTGGCACACACAG
* * * * * * *
44680106 TGCATCATCGGATAAACCAAAGAAAATATACTGGTATACATAG
1 TGCATCATCGGACAAACCGAAGTAATTATACTGGCACACACAG
* * ** *
44680149 TGCATCATCGGACAAGCCGAAATAATTATACTAACACACATAG
1 TGCATCATCGGACAAACCGAAGTAATTATACTGGCACACACAG
* * * ** * * *
44680192 TGCATTATCGAAAAAATTGAATTAATTATACTAGCACCCACAG
1 TGCATCATCGGACAAACCGAAGTAATTATACTGGCACACACAG
* ** * *
44680235 TGCATCATCGAACAAGTCGAAGTAATTATACTGGCACACAGAC
1 TGCATCATCGGACAAACCGAAGTAATTATACTGGCACACACAG
* *
44680278 TACATCATCGGATAAACCGAAGTA
1 TGCATCATCGGACAAACCGAAGTA
44680302 TAACATGTAC
Statistics
Matches: 179, Mismatches: 60, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
43 179 1.00
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.22
Consensus pattern (43 bp):
TGCATCATCGGACAAACCGAAGTAATTATACTGGCACACACAG
Found at i:44689685 original size:44 final size:43
Alignment explanation
Indices: 44689600--44689686 Score: 104
Period size: 43 Copynumber: 2.0 Consensus size: 43
44689590 ATTTAAACTA
* * *
44689600 GTAAACTTCTAGTTTACTATGCATGTGATTCAGCATTACTAAT
1 GTAAACTTCTAGTTTACCATGCATGTGATTAACCATTACTAAT
* *
44689643 GTAAACTTCTGGTTTACCATCGTATGTGATTTAACCA-TACTAAT
1 GTAAACTTCTAGTTTACCAT-GCATGTGA-TTAACCATTACTAAT
44689687 ATATGATAGT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
43 18 0.49
44 14 0.38
45 5 0.14
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (43 bp):
GTAAACTTCTAGTTTACCATGCATGTGATTAACCATTACTAAT
Found at i:44690565 original size:13 final size:13
Alignment explanation
Indices: 44690547--44690579 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
44690537 CAAAATAAAT
44690547 ATTAATTA-ATTAA
1 ATTAATTAGA-TAA
44690560 ATTAATTAGATAA
1 ATTAATTAGATAA
44690573 ATTAATT
1 ATTAATT
44690580 TTTCAATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 18 0.95
14 1 0.05
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (13 bp):
ATTAATTAGATAA
Found at i:44690596 original size:16 final size:18
Alignment explanation
Indices: 44690570--44690602 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
44690560 ATTAATTAGA
44690570 TAAATTAATTTT-TCAAT
1 TAAATTAATTTTCTCAAT
44690587 TAAA-TAATTTTCTCAA
1 TAAATTAATTTTCTCAA
44690603 CCCAATTCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.48
Consensus pattern (18 bp):
TAAATTAATTTTCTCAAT
Found at i:44693488 original size:54 final size:54
Alignment explanation
Indices: 44693403--44693810 Score: 450
Period size: 54 Copynumber: 7.6 Consensus size: 54
44693393 TGGGGTCAAT
*
44693403 AAATGACTGAATTA-CCCCATAGGGTAAAATGAACGAATTACCCTCACAGGGTA
1 AAATGACTGAATTACCCCCATAGGGTAAAATGAACGAATTACCCCCACAGGGTA
* * * *
44693456 AAATGACTAAATTACCCCCACAGGGTAAAATG-ACAGTATTACCCCTACAGGGTA
1 AAATGACTGAATTACCCCCATAGGGTAAAATGAAC-GAATTACCCCCACAGGGTA
* * * * **
44693510 AAATGACCGTATTACCCCCATAGGGTAAAAT-AATCGTATTGCCTTCACAGGGTA
1 AAATGACTGAATTACCCCCATAGGGTAAAATGAA-CGAATTACCCCCACAGGGTA
* * * ** * *
44693564 AAATGACCGTATTACTCCCATAGCCTAAAATGATCGAATTACCCCCATAGGGTA
1 AAATGACTGAATTACCCCCATAGGGTAAAATGAACGAATTACCCCCACAGGGTA
* * * * * *
44693618 AAATGATTGAATTACCCTCACAGGGTAAAATGATCAAATTACCCCCACAAGGTA
1 AAATGACTGAATTACCCCCATAGGGTAAAATGAACGAATTACCCCCACAGGGTA
* * * *
44693672 AAATGACCGAATTACCCCTATAGGGTAAAATGACCGAATTACCCCCACAGGATA
1 AAATGACTGAATTACCCCCATAGGGTAAAATGAACGAATTACCCCCACAGGGTA
* * * * *
44693726 AAATGACTGAATTA-ACCTATAGGGTAAAATGACCGAATTACCCCTATAGGGT-
1 AAATGACTGAATTACCCCCATAGGGTAAAATGAACGAATTACCCCCACAGGGTA
44693778 AAATGA-TCGAATTACCCCCATAGGGTAAAATGA
1 AAATGACT-GAATTACCCCCATAGGGTAAAATGA
44693811 CTATTTTACC
Statistics
Matches: 299, Mismatches: 49, Indels: 14
0.83 0.14 0.04
Matches are distributed among these distances:
51 1 0.00
52 12 0.04
53 65 0.22
54 219 0.73
55 2 0.01
ACGTcount: A:0.38, C:0.22, G:0.17, T:0.22
Consensus pattern (54 bp):
AAATGACTGAATTACCCCCATAGGGTAAAATGAACGAATTACCCCCACAGGGTA
Found at i:44693524 original size:81 final size:80
Alignment explanation
Indices: 44693403--44693811 Score: 445
Period size: 81 Copynumber: 5.1 Consensus size: 80
44693393 TGGGGTCAAT
* * * *
44693403 AAATGACTGAATTACCCC-ATAGGGTAAAATGAACGAATTACCCTCACAGGGTAAAATGACTAAA
1 AAATGACAGAATTACCCCTATAGGGTAAAATGACCGAATTACCC-CATAGGGTAAAATGACTGAA
44693467 TTACCCCCACAGGGTA
65 TTACCCCCACAGGGTA
* * * * *
44693483 AAATGACAGTATTACCCCTACAGGGTAAAATGACCGTATTACCCCCATAGGGTAAAAT-AATCGT
1 AAATGACAGAATTACCCCTATAGGGTAAAATGACCGAATTA-CCCCATAGGGTAAAATGACT-GA
* **
44693547 ATTGCCTTCACAGGGTA
64 ATTACCCCCACAGGGTA
* * ** * *
44693564 AAATGACCGTATTACTCCC-ATAGCCTAAAATGATCGAATTACCCCCATAGGGTAAAATGATTGA
1 AAATGACAGAATTAC-CCCTATAGGGTAAAATGACCGAATTA-CCCCATAGGGTAAAATGACTGA
*
44693628 ATTACCCTCACAGGGTA
64 ATTACCCCCACAGGGTA
* * * *
44693645 AAATGATCA-AATTACCCCCACAAGGTAAAATGACCGAATTACCCCTATAGGGTAAAATGACCGA
1 AAATGA-CAGAATTACCCCTATAGGGTAAAATGACCGAATTACCCC-ATAGGGTAAAATGACTGA
*
44693709 ATTACCCCCACAGGATA
64 ATTACCCCCACAGGGTA
* *
44693726 AAATGACTGAATTA-ACCTATAGGGTAAAATGACCGAATTACCCCTATAGGGT-AAATGA-TCGA
1 AAATGACAGAATTACCCCTATAGGGTAAAATGACCGAATTACCCC-ATAGGGTAAAATGACT-GA
*
44693788 ATTACCCCCATAGGGTA
64 ATTACCCCCACAGGGTA
44693805 AAATGAC
1 AAATGAC
44693812 TATTTTACCC
Statistics
Matches: 278, Mismatches: 41, Indels: 21
0.82 0.12 0.06
Matches are distributed among these distances:
79 30 0.11
80 60 0.22
81 179 0.64
82 9 0.03
ACGTcount: A:0.38, C:0.22, G:0.17, T:0.22
Consensus pattern (80 bp):
AAATGACAGAATTACCCCTATAGGGTAAAATGACCGAATTACCCCATAGGGTAAAATGACTGAAT
TACCCCCACAGGGTA
Found at i:44693822 original size:27 final size:26
Alignment explanation
Indices: 44693403--44693811 Score: 392
Period size: 27 Copynumber: 15.3 Consensus size: 26
44693393 TGGGGTCAAT
44693403 AAATGACTGAATTA-CCCCATAGGGTA
1 AAATGAC-GAATTACCCCCATAGGGTA
* *
44693429 AAATGAACGAATTACCCTCACAGGGTA
1 AAATG-ACGAATTACCCCCATAGGGTA
* *
44693456 AAATGACTAAATTACCCCCACAGGGTA
1 AAATGAC-GAATTACCCCCATAGGGTA
* * *
44693483 AAATGACAGTATTACCCCTACAGGGTA
1 AAATGAC-GAATTACCCCCATAGGGTA
*
44693510 AAATGACCGTATTACCCCCATAGGGTA
1 AAATGA-CGAATTACCCCCATAGGGTA
* * * ** *
44693537 AAATAATCGTATTGCCTTCACAGGGTA
1 AAATGA-CGAATTACCCCCATAGGGTA
* * **
44693564 AAATGACCGTATTACTCCCATAGCCTA
1 AAATGA-CGAATTACCCCCATAGGGTA
44693591 AAATGATCGAATTACCCCCATAGGGTA
1 AAATGA-CGAATTACCCCCATAGGGTA
* * *
44693618 AAATGATTGAATTACCCTCACAGGGTA
1 AAATGA-CGAATTACCCCCATAGGGTA
* * *
44693645 AAATGATCAAATTACCCCCACAAGGTA
1 AAATGA-CGAATTACCCCCATAGGGTA
*
44693672 AAATGACCGAATTACCCCTATAGGGTA
1 AAATGA-CGAATTACCCCCATAGGGTA
* *
44693699 AAATGACCGAATTACCCCCACAGGATA
1 AAATGA-CGAATTACCCCCATAGGGTA
* *
44693726 AAATGACTGAATTA-ACCTATAGGGTA
1 AAATGAC-GAATTACCCCCATAGGGTA
*
44693752 AAATGACCGAATTACCCCTATAGGGT-
1 AAATGA-CGAATTACCCCCATAGGGTA
44693778 AAATGATCGAATTACCCCCATAGGGTA
1 AAATGA-CGAATTACCCCCATAGGGTA
44693805 AAATGAC
1 AAATGAC
44693812 TATTTTACCC
Statistics
Matches: 323, Mismatches: 52, Indels: 16
0.83 0.13 0.04
Matches are distributed among these distances:
26 59 0.18
27 263 0.81
28 1 0.00
ACGTcount: A:0.38, C:0.22, G:0.17, T:0.22
Consensus pattern (26 bp):
AAATGACGAATTACCCCCATAGGGTA
Found at i:44694000 original size:26 final size:26
Alignment explanation
Indices: 44693970--44694024 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
44693960 TGGAGGAAGT
* *
44693970 ATACTGTTACTGACAGCTTTGTTGCG
1 ATACTGTTACTGACAACTTTGCTGCG
*
44693996 ATACTGTTACTGGCAACTTTGCTGCG
1 ATACTGTTACTGACAACTTTGCTGCG
44694022 ATA
1 ATA
44694025 TTGGTGTGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (26 bp):
ATACTGTTACTGACAACTTTGCTGCG
Found at i:44694175 original size:28 final size:27
Alignment explanation
Indices: 44694132--44694192 Score: 95
Period size: 28 Copynumber: 2.2 Consensus size: 27
44694122 ACTGTATCGA
*
44694132 TACTGTATTGGACTAAGGCCCACATTG
1 TACTGTATTGGACTAAGGCCCACACTG
*
44694159 TTACTGTATTGGGCTAAGGCCCACACTG
1 -TACTGTATTGGACTAAGGCCCACACTG
44694187 TACTGT
1 TACTGT
44694193 TACTGAATAG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 6 0.19
28 25 0.81
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (27 bp):
TACTGTATTGGACTAAGGCCCACACTG
Found at i:44694206 original size:33 final size:34
Alignment explanation
Indices: 44694157--44694225 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 34
44694147 AGGCCCACAT
* *
44694157 TGTTACTGTATTGGGCTAAGGCCCACACTG-TAC
1 TGTTACTGAATAGGGCTAAGGCCCACACTGTTAC
* *
44694190 TGTTACTGAATAGGGCTCAGGCCCAGACTGTTAC
1 TGTTACTGAATAGGGCTAAGGCCCACACTGTTAC
44694224 TG
1 TG
44694226 CATGTTGTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
33 26 0.84
34 5 0.16
ACGTcount: A:0.22, C:0.23, G:0.26, T:0.29
Consensus pattern (34 bp):
TGTTACTGAATAGGGCTAAGGCCCACACTGTTAC
Found at i:44705568 original size:20 final size:20
Alignment explanation
Indices: 44705545--44705589 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
44705535 CCAGCATGTC
44705545 ATAAAATATAAGAAAAAGGA
1 ATAAAATATAAGAAAAAGGA
44705565 ATAAAATATAAGAAAAAGGA
1 ATAAAATATAAGAAAAAGGA
44705585 ATAAA
1 ATAAA
44705590 CTTTAGGGGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.71, C:0.00, G:0.13, T:0.16
Consensus pattern (20 bp):
ATAAAATATAAGAAAAAGGA
Found at i:44707253 original size:31 final size:31
Alignment explanation
Indices: 44707212--44707273 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
44707202 AATGTGTTAG
44707212 TGAATGACATATTTGTAAATTAACATTCGAA
1 TGAATGACATATTTGTAAATTAACATTCGAA
*
44707243 TGAATTACATATTTGTAAATTAACATTCGAA
1 TGAATGACATATTTGTAAATTAACATTCGAA
44707274 GTTCAGTAAG
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:0.42, C:0.10, G:0.11, T:0.37
Consensus pattern (31 bp):
TGAATGACATATTTGTAAATTAACATTCGAA
Found at i:44712403 original size:22 final size:22
Alignment explanation
Indices: 44712372--44712538 Score: 160
Period size: 25 Copynumber: 7.1 Consensus size: 22
44712362 GTGTTATAGA
44712372 TTTAATGTATAATGCTGTCAAAT
1 TTTAATGTATAATGCTGTC-AAT
*
44712395 TTTAA-GTATATTGATGCTGTCCAT
1 TTTAATGTATA---ATGCTGTCAAT
44712419 TTTAATGTATAATGCTGTCCAAT
1 TTTAATGTATAATGCTGT-CAAT
* *
44712442 CTTAA-GTATATTGATGCTGTCCAT
1 TTTAATGTATA---ATGCTGTCAAT
44712466 TTTAATGTATAATGCTGTCCAAT
1 TTTAATGTATAATGCTGT-CAAT
*
44712489 TTTAA-GTATATTGATGCTGTCCAT
1 TTTAATGTATA---ATGCTGTCAAT
44712513 TTTAATGTATAATGCTGTCCAAT
1 TTTAATGTATAATGCTGT-CAAT
44712536 TTT
1 TTT
44712539 GAGTATATTT
Statistics
Matches: 121, Mismatches: 8, Indels: 30
0.76 0.05 0.19
Matches are distributed among these distances:
22 36 0.30
23 26 0.21
24 22 0.18
25 37 0.31
ACGTcount: A:0.28, C:0.13, G:0.14, T:0.45
Consensus pattern (22 bp):
TTTAATGTATAATGCTGTCAAT
Found at i:44712447 original size:47 final size:47
Alignment explanation
Indices: 44712372--44712628 Score: 340
Period size: 47 Copynumber: 5.5 Consensus size: 47
44712362 GTGTTATAGA
*
44712372 TTTAATGTATAATGCTGTCAAATTTTAAGTATATTGATGCTGTCCAT
1 TTTAATGTATAATGCTGTCCAATTTTAAGTATATTGATGCTGTCCAT
*
44712419 TTTAATGTATAATGCTGTCCAATCTTAAGTATATTGATGCTGTCCAT
1 TTTAATGTATAATGCTGTCCAATTTTAAGTATATTGATGCTGTCCAT
44712466 TTTAATGTATAATGCTGTCCAATTTTAAGTATATTGATGCTGTCCAT
1 TTTAATGTATAATGCTGTCCAATTTTAAGTATATTGATGCTGTCCAT
* * * * *
44712513 TTTAATGTATAATGCTGTCCAATTTTGAGTATATTTAAGCTGTCTAA
1 TTTAATGTATAATGCTGTCCAATTTTAAGTATATTGATGCTGTCCAT
** * *
44712560 TTCGATGTATAATGCTGTCC-A-TTTAGAGCATATT-ATTGCTGTCCAA
1 TTTAATGTATAATGCTGTCCAATTTTA-AGTATATTGA-TGCTGTCCAT
* * *
44712606 TTTCATGAATAATTGTTGTCCAA
1 TTTAATGTATAA-TGCTGTCCAA
44712629 AATAGGGTTG
Statistics
Matches: 188, Mismatches: 18, Indels: 7
0.88 0.08 0.03
Matches are distributed among these distances:
45 4 0.02
46 25 0.13
47 158 0.84
48 1 0.01
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.43
Consensus pattern (47 bp):
TTTAATGTATAATGCTGTCCAATTTTAAGTATATTGATGCTGTCCAT
Found at i:44718657 original size:22 final size:22
Alignment explanation
Indices: 44718579--44718658 Score: 90
Period size: 22 Copynumber: 3.5 Consensus size: 22
44718569 GTGTTATAAA
*
44718579 TTTAATGTATAATGCTGTCAAAT
1 TTTAA-GTATAATGCTGTCCAAT
44718602 TTTAAGTATATTGATGCTGTCC-AT
1 TTTAAGTATA---ATGCTGTCCAAT
44718626 TTTAATGTATAATGCTGTCCAAT
1 TTTAA-GTATAATGCTGTCCAAT
*
44718649 TTTGAGTATA
1 TTTAAGTATA
44718659 TTATATATAA
Statistics
Matches: 50, Mismatches: 2, Indels: 11
0.79 0.03 0.17
Matches are distributed among these distances:
22 19 0.38
23 11 0.22
24 7 0.14
25 13 0.26
ACGTcount: A:0.30, C:0.10, G:0.15, T:0.45
Consensus pattern (22 bp):
TTTAAGTATAATGCTGTCCAAT
Found at i:44718668 original size:31 final size:31
Alignment explanation
Indices: 44718633--44718691 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
44718623 CATTTTAATG
*
44718633 TATAATGCTGTCCAATTTTGAGTATATTATA
1 TATAATGCTGTCCAATTTTAAGTATATTATA
44718664 TATAATGCTGTCCAATTTTAAGTATATT
1 TATAATGCTGTCCAATTTTAAGTATATT
44718692 GATGTTGTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.32, C:0.10, G:0.12, T:0.46
Consensus pattern (31 bp):
TATAATGCTGTCCAATTTTAAGTATATTATA
Found at i:44718715 original size:78 final size:78
Alignment explanation
Indices: 44718586--44718738 Score: 279
Period size: 78 Copynumber: 2.0 Consensus size: 78
44718576 AAATTTAATG
44718586 TATAATGCTGTCAAATTTTAAGTATATTGATGCTGTCCATTTTAATGTATAATGCTGTCCAATTT
1 TATAATGCTGTCAAATTTTAAGTATATTGATGCTGTCCATTTTAATGTATAATGCTGTCCAATTT
44718651 TGAGTATATTATA
66 TGAGTATATTATA
* * *
44718664 TATAATGCTGTCCAATTTTAAGTATATTGATGTTGTCTATTTTAATGTATAATGCTGTCCAATTT
1 TATAATGCTGTCAAATTTTAAGTATATTGATGCTGTCCATTTTAATGTATAATGCTGTCCAATTT
44718729 TGAGTATATT
66 TGAGTATATT
44718739 TAAGCTGTCT
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
78 72 1.00
ACGTcount: A:0.29, C:0.10, G:0.14, T:0.46
Consensus pattern (78 bp):
TATAATGCTGTCAAATTTTAAGTATATTGATGCTGTCCATTTTAATGTATAATGCTGTCCAATTT
TGAGTATATTATA
Found at i:44718735 original size:22 final size:22
Alignment explanation
Indices: 44718664--44718799 Score: 71
Period size: 25 Copynumber: 5.8 Consensus size: 22
44718654 GTATATTATA
*
44718664 TATAATGCTGTCCAATTTTAAG
1 TATAATGCTGTCCAATTTTGAG
* * *
44718686 TATATTGATGTTGT-CTATTTTAATG
1 TATA---ATGCTGTCCAATTTTGA-G
44718711 TATAATGCTGTCCAATTTTGAG
1 TATAATGCTGTCCAATTTTGAG
* * *
44718733 TATATTTAAGCTGTCTAA-TTCGATG
1 TATA---ATGCTGTCCAATTTTGA-G
*
44718758 TATAATGCTGTCC-ATTTAGAG
1 TATAATGCTGTCCAATTTTGAG
*
44718779 CATATTATTGCTGTCCAATTT
1 --TA-TAATGCTGTCCAATTT
44718800 GATGAATAAT
Statistics
Matches: 88, Mismatches: 12, Indels: 25
0.70 0.10 0.20
Matches are distributed among these distances:
21 2 0.02
22 26 0.30
23 9 0.10
24 22 0.25
25 29 0.33
ACGTcount: A:0.27, C:0.12, G:0.15, T:0.45
Consensus pattern (22 bp):
TATAATGCTGTCCAATTTTGAG
Found at i:44718735 original size:47 final size:47
Alignment explanation
Indices: 44718664--44718784 Score: 154
Period size: 47 Copynumber: 2.6 Consensus size: 47
44718654 GTATATTATA
* * * * *
44718664 TATAATGCTGTCCAATTTTAAGTATATTGATGTTGTCTATTTTAATG
1 TATAATGCTGTCCAATTTTGAGTATATTGAAGCTGTCTAATTCAATG
* *
44718711 TATAATGCTGTCCAATTTTGAGTATATTTAAGCTGTCTAATTCGATG
1 TATAATGCTGTCCAATTTTGAGTATATTGAAGCTGTCTAATTCAATG
* *
44718758 TATAATGCTGTCC-ATTTAGAGCATATT
1 TATAATGCTGTCCAATTTTGAGTATATT
44718785 ATTGCTGTCC
Statistics
Matches: 65, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
46 12 0.18
47 53 0.82
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.45
Consensus pattern (47 bp):
TATAATGCTGTCCAATTTTGAGTATATTGAAGCTGTCTAATTCAATG
Found at i:44718809 original size:46 final size:46
Alignment explanation
Indices: 44718712--44718818 Score: 117
Period size: 46 Copynumber: 2.3 Consensus size: 46
44718702 ATTTTAATGT
* * * *
44718712 ATAATGCTGTCCAATTTTGAGTATATTTAAGCTGTCTAATTCGATGT
1 ATAATGCTGTCC-ATTTAGAGCATATTTAAGCTGTCCAATTCGATGA
* *
44718759 ATAATGCTGTCCATTTAGAGCATA-TTATTGCTGTCCAATTTGATGA
1 ATAATGCTGTCCATTTAGAGCATATTTA-AGCTGTCCAATTCGATGA
*
44718805 ATAATTACTGTCCA
1 ATAA-TGCTGTCCA
44718819 AAATAGGGTT
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
45 3 0.06
46 28 0.55
47 20 0.39
ACGTcount: A:0.29, C:0.15, G:0.16, T:0.40
Consensus pattern (46 bp):
ATAATGCTGTCCATTTAGAGCATATTTAAGCTGTCCAATTCGATGA
Found at i:44722286 original size:3 final size:3
Alignment explanation
Indices: 44722278--44722308 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
44722268 ATGGCAAATC
*
44722278 ACA ACA ACA ACA ACA ACA ACA ACA CCA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA A
44722309 GGTGAGCTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.65, C:0.35, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:44730648 original size:2 final size:2
Alignment explanation
Indices: 44730641--44730682 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
44730631 AAATCCTACC
44730641 AT AT AT AT AT AT 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 AT AT AT AT AT AT
44730683 CAAACTTACC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:44731611 original size:44 final size:44
Alignment explanation
Indices: 44731436--44731600 Score: 126
Period size: 43 Copynumber: 3.8 Consensus size: 44
44731426 AATGCAAAAC
* * *
44731436 GTCCCAGACGTGGTCTTACATG-AAATCA-AATATCAATGCCACT
1 GTCCCAGACATGGTCTTACACGTAAATCACAA-ATCAATGCCAAT
* * ** * * **
44731479 GTCCCCA-ACAGGGTCTTACACG-AACTCGTATAT-GATGCGGAT
1 GT-CCCAGACATGGTCTTACACGTAAATCACAAATCAATGCCAAT
* * *
44731521 GTCCTAGACATGGTCTTACACGTAAATTACAAATCGATGCCAAT
1 GTCCCAGACATGGTCTTACACGTAAATCACAAATCAATGCCAAT
* *
44731565 GTCCCAGACGTGGTCTTACACGT-AATCACATATCAA
1 GTCCCAGACATGGTCTTACACGTAAATCACAAATCAA
44731601 AATCCTATGT
Statistics
Matches: 93, Mismatches: 24, Indels: 10
0.73 0.19 0.08
Matches are distributed among these distances:
41 3 0.03
42 21 0.23
43 36 0.39
44 33 0.35
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.25
Consensus pattern (44 bp):
GTCCCAGACATGGTCTTACACGTAAATCACAAATCAATGCCAAT
Found at i:44733654 original size:21 final size:21
Alignment explanation
Indices: 44733613--44733664 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 21
44733603 TATAGATACA
44733613 AATTTTATTTTTAGTCATATT
1 AATTTTATTTTTAGTCATATT
*
44733634 -ATTTTATTTTTTG-CACTTATT
1 AATTTTATTTTTAGTCA--TATT
44733655 AATTTTATTT
1 AATTTTATTT
44733665 CCACTACTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 2 0.07
20 12 0.44
21 4 0.15
22 9 0.33
ACGTcount: A:0.25, C:0.06, G:0.04, T:0.65
Consensus pattern (21 bp):
AATTTTATTTTTAGTCATATT
Found at i:44743174 original size:14 final size:14
Alignment explanation
Indices: 44743131--44743176 Score: 58
Period size: 14 Copynumber: 3.2 Consensus size: 14
44743121 CCCATTTACC
44743131 CCTCCTCTCCCTTT
1 CCTCCTCTCCCTTT
*
44743145 CTTCTCC-CTCCATTT
1 C--CTCCTCTCCCTTT
44743160 CCTCCTCTCCCTTT
1 CCTCCTCTCCCTTT
44743174 CCT
1 CCT
44743177 TGTTGGTTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
13 4 0.15
14 11 0.41
15 8 0.30
16 4 0.15
ACGTcount: A:0.02, C:0.54, G:0.00, T:0.43
Consensus pattern (14 bp):
CCTCCTCTCCCTTT
Found at i:44750481 original size:23 final size:23
Alignment explanation
Indices: 44750440--44750532 Score: 123
Period size: 23 Copynumber: 4.0 Consensus size: 23
44750430 ACCTGATTAG
** *
44750440 TATACGACACACGAGGTGCCTGA
1 TATACGACACATAAAGTGCCTGA
* *
44750463 AATATGACACATAAAGTGCCTGA
1 TATACGACACATAAAGTGCCTGA
* *
44750486 TATACAACACATAAAGTACCTGA
1 TATACGACACATAAAGTGCCTGA
44750509 TATACGACACATAAAGTGCCTGA
1 TATACGACACATAAAGTGCCTGA
44750532 T
1 T
44750533 CAGCAAGGCA
Statistics
Matches: 59, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 59 1.00
ACGTcount: A:0.40, C:0.22, G:0.17, T:0.22
Consensus pattern (23 bp):
TATACGACACATAAAGTGCCTGA
Found at i:44751178 original size:19 final size:19
Alignment explanation
Indices: 44751154--44751191 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
44751144 TTTTAGTCCC
44751154 TAAAACATAAAACTTATAG
1 TAAAACATAAAACTTATAG
44751173 TAAAACATAAAACTTATAG
1 TAAAACATAAAACTTATAG
44751192 CTTACTTCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.58, C:0.11, G:0.05, T:0.26
Consensus pattern (19 bp):
TAAAACATAAAACTTATAG
Found at i:44751514 original size:27 final size:25
Alignment explanation
Indices: 44751467--44751518 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 25
44751457 GTTCGAATGG
44751467 CTTCTTGTTCTTTTTGTTTCTTTTA
1 CTTCTTGTTCTTTTTGTTTCTTTTA
44751492 CTTCTT-TTCTTTCTTTAGTTTCTTTTA
1 CTTCTTGTTC-TT-TTT-GTTTCTTTTA
44751519 TTTACTTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
24 3 0.12
25 8 0.33
26 3 0.12
27 10 0.42
ACGTcount: A:0.06, C:0.17, G:0.06, T:0.71
Consensus pattern (25 bp):
CTTCTTGTTCTTTTTGTTTCTTTTA
Found at i:44751537 original size:14 final size:14
Alignment explanation
Indices: 44751517--44751543 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
44751507 TAGTTTCTTT
44751517 TATTTACTTTATTC
1 TATTTACTTTATTC
44751531 TATTTACTTTATT
1 TATTTACTTTATT
44751544 GTTTTAATTA
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:0.22, C:0.11, G:0.00, T:0.67
Consensus pattern (14 bp):
TATTTACTTTATTC
Found at i:44755589 original size:16 final size:16
Alignment explanation
Indices: 44755554--44755607 Score: 81
Period size: 16 Copynumber: 3.2 Consensus size: 16
44755544 TCCATCCTTG
44755554 CCCTCCTTTCTTCCTTCC
1 CCCT-CTTT-TTCCTTCC
*
44755572 CCCTCTTTTTCATTCC
1 CCCTCTTTTTCCTTCC
44755588 CCCTCTTTTTCCTTCC
1 CCCTCTTTTTCCTTCC
44755604 CCCT
1 CCCT
44755608 TACCGAACAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
16 26 0.76
17 4 0.12
18 4 0.12
ACGTcount: A:0.02, C:0.52, G:0.00, T:0.46
Consensus pattern (16 bp):
CCCTCTTTTTCCTTCC
Found at i:44757370 original size:6 final size:6
Alignment explanation
Indices: 44757359--44757404 Score: 74
Period size: 6 Copynumber: 7.5 Consensus size: 6
44757349 TTTGTCTTTT
*
44757359 TTTTAG TTTTAG TTTTAG TTTTAG TTTTAG TTTTAT TTTTATG TTT
1 TTTTAG TTTTAG TTTTAG TTTTAG TTTTAG TTTTAG TTTTA-G TTT
44757405 ATTTTATTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
6 34 0.92
7 3 0.08
ACGTcount: A:0.15, C:0.00, G:0.13, T:0.72
Consensus pattern (6 bp):
TTTTAG
Found at i:44757405 original size:6 final size:5
Alignment explanation
Indices: 44757340--44757414 Score: 62
Period size: 6 Copynumber: 13.6 Consensus size: 5
44757330 ATGAAGATCG
*
44757340 TTTAT TTTAT TTGTCT TTT-T TTTAGT TTTAGT TTTAGT TTTAGT TTTAGT
1 TTTAT TTTAT TT-TAT TTTAT TTTA-T TTTA-T TTTA-T TTTA-T TTTA-T
44757390 TTTATT TTTAT GTTTAT TTTAT TTT
1 TTTA-T TTTAT -TTTAT TTTAT TTT
44757415 CTTAGACTTA
Statistics
Matches: 64, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
4 4 0.06
5 17 0.27
6 43 0.67
ACGTcount: A:0.15, C:0.01, G:0.09, T:0.75
Consensus pattern (5 bp):
TTTAT
Found at i:44757405 original size:18 final size:18
Alignment explanation
Indices: 44757358--44757414 Score: 82
Period size: 18 Copynumber: 3.2 Consensus size: 18
44757348 ATTTGTCTTT
44757358 TTTTTAGTTTTAGTTTTA
1 TTTTTAGTTTTAGTTTTA
*
44757376 GTTTTAGTTTTAGTTTTA
1 TTTTTAGTTTTAGTTTTA
44757394 TTTTTA-TGTTTA-TTTTA
1 TTTTTAGT-TTTAGTTTTA
44757411 TTTT
1 TTTT
44757415 CTTAGACTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
17 10 0.28
18 26 0.72
ACGTcount: A:0.16, C:0.00, G:0.11, T:0.74
Consensus pattern (18 bp):
TTTTTAGTTTTAGTTTTA
Found at i:44758727 original size:24 final size:24
Alignment explanation
Indices: 44758699--44758746 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
44758689 GTTTGAGCAG
44758699 TTTCATCATCAAGCTGAGCGTATA
1 TTTCATCATCAAGCTGAGCGTATA
44758723 TTTCATCATCAAGCTGAGCGTATA
1 TTTCATCATCAAGCTGAGCGTATA
44758747 CTTAGTTGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (24 bp):
TTTCATCATCAAGCTGAGCGTATA
Found at i:44760411 original size:18 final size:19
Alignment explanation
Indices: 44760390--44760458 Score: 61
Period size: 19 Copynumber: 3.6 Consensus size: 19
44760380 TAGAAATTCT
*
44760390 AAAATTTAT-ATTTTTTAA
1 AAAATTTATAAATTTTTAA
*
44760408 AAAAATTATAAATTTTTAA
1 AAAATTTATAAATTTTTAA
* * *
44760427 AAAATCTA-AAATATATATA
1 AAAATTTATAAATTTTTA-A
44760446 AAAATTTAATAAA
1 AAAATTT-ATAAA
44760459 ATAATAATTT
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
18 15 0.38
19 21 0.52
20 1 0.03
21 3 0.08
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (19 bp):
AAAATTTATAAATTTTTAA
Found at i:44760782 original size:21 final size:21
Alignment explanation
Indices: 44760758--44760798 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
44760748 CCTTTTTCTA
*
44760758 AAGTTAAAAGTCAAAACTATC
1 AAGTTAAAAGACAAAACTATC
44760779 AAGTTAAAAGACAAAACTAT
1 AAGTTAAAAGACAAAACTAT
44760799 ATTGTTTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.56, C:0.12, G:0.10, T:0.22
Consensus pattern (21 bp):
AAGTTAAAAGACAAAACTATC
Found at i:44763450 original size:19 final size:18
Alignment explanation
Indices: 44763428--44763478 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
44763418 TTTTTTATAT
44763428 TTTTTAAATTTTAAATAAC
1 TTTTTAAATTTTAAAT-AC
*
44763447 TTTTTAGAATTTTTACATAC
1 TTTTTA-AA-TTTTAAATAC
*
44763467 TTTTTGAATTTT
1 TTTTTAAATTTT
44763479 GAAAAATGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
18 4 0.14
19 8 0.29
20 9 0.32
21 7 0.25
ACGTcount: A:0.31, C:0.06, G:0.04, T:0.59
Consensus pattern (18 bp):
TTTTTAAATTTTAAATAC
Found at i:44763457 original size:20 final size:19
Alignment explanation
Indices: 44763428--44763478 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
44763418 TTTTTTATAT
44763428 TTTTTA-AATTTTAAATAAC
1 TTTTTAGAATTTTAAAT-AC
*
44763447 TTTTTAGAATTTTTACATAC
1 TTTTTAGAA-TTTTAAATAC
44763467 TTTTT-GAATTTT
1 TTTTTAGAATTTT
44763479 GAAAAATGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 4 0.14
19 9 0.31
20 9 0.31
21 7 0.24
ACGTcount: A:0.31, C:0.06, G:0.04, T:0.59
Consensus pattern (19 bp):
TTTTTAGAATTTTAAATAC
Found at i:44763525 original size:10 final size:10
Alignment explanation
Indices: 44763511--44763567 Score: 53
Period size: 10 Copynumber: 5.7 Consensus size: 10
44763501 ATGTTTTTTC
*
44763511 ATTTTCATA-
1 ATTTTTATAT
44763520 ATTTTTATAT
1 ATTTTTATAT
44763530 ATTTTTATAT
1 ATTTTTATAT
* *
44763540 ATTTATAATTT
1 ATTT-TTATAT
*
44763551 GTTTTTATAT
1 ATTTTTATAT
*
44763561 GTTTTTA
1 ATTTTTA
44763568 CATTTAAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
9 8 0.20
10 25 0.62
11 7 0.17
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.67
Consensus pattern (10 bp):
ATTTTTATAT
Found at i:44763667 original size:19 final size:19
Alignment explanation
Indices: 44763623--44763669 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
44763613 ATATATATTT
*
44763623 ATGATTTTTACATTTTTAAA
1 ATGATTTTTACAATTTT-AA
44763643 AT-ATTTTCTACAATTTT-A
1 ATGATTTT-TACAATTTTAA
44763661 ATGATTTTT
1 ATGATTTTT
44763670 TTGGTAAGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
18 4 0.17
19 10 0.42
20 10 0.42
ACGTcount: A:0.32, C:0.06, G:0.04, T:0.57
Consensus pattern (19 bp):
ATGATTTTTACAATTTTAA
Found at i:44770970 original size:96 final size:96
Alignment explanation
Indices: 44770806--44770998 Score: 307
Period size: 96 Copynumber: 2.0 Consensus size: 96
44770796 AACTCAGTTA
* *
44770806 TGAATTTTATTAATAATATAGATAATATATACAATTAATGGAGGTAATCAAGTGTGCATAGTAAA
1 TGAATTTTATTAATAATATAGATAAAATATACAATTAATGGAGGTAATCAAGTGTACATAGTAAA
* *
44770871 ATTAAAATGTATAAAAATGTTAAAATGAAAC
66 ATTAAAATGTATAAAAATATTAAAATAAAAC
* *
44770902 TGAATTTTATTAATAGTATAGATAAAATATACAATTGATGGAGGTAATCAAGTGTACAT-GATAA
1 TGAATTTTATTAATAATATAGATAAAATATACAATTAATGGAGGTAATCAAGTGTACATAG-TAA
*
44770966 AATTAAAATGTATCAAAATATTAAAATAAAAC
65 AATTAAAATGTATAAAAATATTAAAATAAAAC
44770998 T
1 T
44770999 TTAATTGAGT
Statistics
Matches: 89, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
95 1 0.01
96 88 0.99
ACGTcount: A:0.49, C:0.05, G:0.13, T:0.33
Consensus pattern (96 bp):
TGAATTTTATTAATAATATAGATAAAATATACAATTAATGGAGGTAATCAAGTGTACATAGTAAA
ATTAAAATGTATAAAAATATTAAAATAAAAC
Found at i:44783783 original size:33 final size:33
Alignment explanation
Indices: 44783746--44783812 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
44783736 AATTTGAAAG
44783746 TTCTCTCTCGAAAATTACCTTGAAAATAACGTC
1 TTCTCTCTCGAAAATTACCTTGAAAATAACGTC
*
44783779 TTCTCTCTCGAAAATTACCTTGAAAGTAACGTC
1 TTCTCTCTCGAAAATTACCTTGAAAATAACGTC
44783812 T
1 T
44783813 CAGTTTTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.31, C:0.24, G:0.10, T:0.34
Consensus pattern (33 bp):
TTCTCTCTCGAAAATTACCTTGAAAATAACGTC
Found at i:44793911 original size:2 final size:2
Alignment explanation
Indices: 44793899--44793937 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
44793889 GAAATACCTT
*
44793899 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
44793938 AAATCTAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:44793980 original size:24 final size:23
Alignment explanation
Indices: 44793934--44793992 Score: 73
Period size: 23 Copynumber: 2.4 Consensus size: 23
44793924 ATATATATAA
* *
44793934 TATAAAATCTAATATTTTCAAAAAGT
1 TATAAAA--TAATATATT-AAAAAAT
44793960 TATAAAATAATATATTAAAAAAT
1 TATAAAATAATATATTAAAAAAT
44793983 TATAAAATAA
1 TATAAAATAA
44793993 AGTATCAAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
23 16 0.52
24 8 0.26
26 7 0.23
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.36
Consensus pattern (23 bp):
TATAAAATAATATATTAAAAAAT
Found at i:44811772 original size:30 final size:31
Alignment explanation
Indices: 44811716--44811797 Score: 105
Period size: 31 Copynumber: 2.7 Consensus size: 31
44811706 AATCTCAAAA
* * *
44811716 TTACACATGAAA-TTTGGTTTCATGTGCAATT
1 TTACACATAAAATTTTGATTT-TTGTGCAATT
44811747 TTACACA-AAAATTTTGATTTTTGTGCAATT
1 TTACACATAAAATTTTGATTTTTGTGCAATT
*
44811777 TTATACATAAAATTTTGATTT
1 TTACACATAAAATTTTGATTT
44811798 GATTTAATTA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
30 18 0.40
31 27 0.60
ACGTcount: A:0.33, C:0.10, G:0.11, T:0.46
Consensus pattern (31 bp):
TTACACATAAAATTTTGATTTTTGTGCAATT
Found at i:44812154 original size:23 final size:24
Alignment explanation
Indices: 44812119--44812171 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
44812109 AACTAATTTT
* *
44812119 TAAAATTTCATAAAATAAAA-AAA
1 TAAATTTTAATAAAATAAAATAAA
*
44812142 TAAATTTTAATAAATTAAAATAAA
1 TAAATTTTAATAAAATAAAATAAA
*
44812166 TGAATT
1 TAAATT
44812172 AACTCTTTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
23 17 0.68
24 8 0.32
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (24 bp):
TAAATTTTAATAAAATAAAATAAA
Found at i:44819179 original size:21 final size:22
Alignment explanation
Indices: 44819150--44819196 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
44819140 CAGAAGGAGT
44819150 GAGTAGTACTTCACAGCAGGTG
1 GAGTAGTACTTCACAGCAGGTG
*
44819172 GAGT-GTACTTCGCAGCAGGTG
1 GAGTAGTACTTCACAGCAGGTG
44819193 GAGT
1 GAGT
44819197 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.23, C:0.17, G:0.36, T:0.23
Consensus pattern (22 bp):
GAGTAGTACTTCACAGCAGGTG
Found at i:44822070 original size:16 final size:16
Alignment explanation
Indices: 44822049--44822085 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
44822039 TTGGTTCGCT
44822049 GTAATGGAATAGAGGC
1 GTAATGGAATAGAGGC
44822065 GTAATGGAATAGAGGC
1 GTAATGGAATAGAGGC
44822081 GTAAT
1 GTAAT
44822086 AGGTAATTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.38, C:0.05, G:0.35, T:0.22
Consensus pattern (16 bp):
GTAATGGAATAGAGGC
Found at i:44822154 original size:44 final size:46
Alignment explanation
Indices: 44822065--44822155 Score: 159
Period size: 46 Copynumber: 2.0 Consensus size: 46
44822055 GAATAGAGGC
*
44822065 GTAATGGAATAGAGGCGTAATAGGTAATTCTTTTGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAAT
44822111 GTAATGGAATAGAGGCGTAAT-GGT-ATTCTTGTGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAAT
44822155 G
1 G
44822156 GAATAGATGT
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
44 20 0.45
45 3 0.07
46 21 0.48
ACGTcount: A:0.26, C:0.04, G:0.31, T:0.38
Consensus pattern (46 bp):
GTAATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAAT
Found at i:44822170 original size:39 final size:44
Alignment explanation
Indices: 44822065--44822172 Score: 136
Period size: 46 Copynumber: 2.5 Consensus size: 44
44822055 GAATAGAGGC
*
44822065 GTAATGGAATAGAGGCGTAATAGGTAATTCTTTTGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTT--AT
44822111 GTAATGGAATAGAGGCGTAAT-GGT-ATTCTTGTGTTTGG-T-T
1 GTAATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTAT
* *
44822151 G-AATGGAATAGATGTGTAATAG
1 GTAATGGAATAGAGGCGTAATAG
44822173 CATAAGGAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
39 17 0.29
40 3 0.05
43 1 0.02
44 13 0.22
45 3 0.05
46 21 0.36
ACGTcount: A:0.29, C:0.04, G:0.31, T:0.37
Consensus pattern (44 bp):
GTAATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTAT
Found at i:44822360 original size:17 final size:17
Alignment explanation
Indices: 44822314--44822353 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
44822304 CATAATTGTT
44822314 ATAAAA-ATATAATTTA
1 ATAAAATATATAATTTA
44822330 ATAAAATATATAATTTA
1 ATAAAATATATAATTTA
44822347 ATAAAAT
1 ATAAAAT
44822354 TGTTAATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 6 0.26
17 17 0.74
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
ATAAAATATATAATTTA
Found at i:44822425 original size:20 final size:21
Alignment explanation
Indices: 44822386--44822425 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
44822376 AATTTACTAA
*
44822386 TAAAATCATAATATATAATAC
1 TAAAATCATAATATAAAATAC
*
44822407 TAAAAT-ATAATTTAAAATA
1 TAAAATCATAATATAAAATA
44822426 ATTANNNNNN
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (21 bp):
TAAAATCATAATATAAAATAC
Found at i:44824421 original size:29 final size:29
Alignment explanation
Indices: 44824400--44824458 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
44824390 CATTTTGATG
44824400 TATTTTGATGTATTTCAATCATTATCGAT
1 TATTTTGATGTATTTCAATCATTATCGAT
44824429 TATTTTGATGTATTTCAATCATTATCGAT
1 TATTTTGATGTATTTCAATCATTATCGAT
44824458 T
1 T
44824459 TATATAGTCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.27, C:0.10, G:0.10, T:0.53
Consensus pattern (29 bp):
TATTTTGATGTATTTCAATCATTATCGAT
Found at i:44824855 original size:25 final size:25
Alignment explanation
Indices: 44824821--44824882 Score: 115
Period size: 25 Copynumber: 2.5 Consensus size: 25
44824811 CAATTTACTG
44824821 GAATTGCAACTATAAAAAACCTCTT
1 GAATTGCAACTATAAAAAACCTCTT
*
44824846 GAATTGCAACTATAAAATACCTCTT
1 GAATTGCAACTATAAAAAACCTCTT
44824871 GAATTGCAACTA
1 GAATTGCAACTA
44824883 GAGCTTCAGC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.42, C:0.19, G:0.10, T:0.29
Consensus pattern (25 bp):
GAATTGCAACTATAAAAAACCTCTT
Found at i:44825141 original size:12 final size:12
Alignment explanation
Indices: 44825124--44825157 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
44825114 CCGCATTTTA
44825124 AGCAAAAGAACG
1 AGCAAAAGAACG
44825136 AGCAAAAGAACG
1 AGCAAAAGAACG
44825148 AGCAAAAGAA
1 AGCAAAAGAA
44825158 AAGAAAGAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.62, C:0.15, G:0.24, T:0.00
Consensus pattern (12 bp):
AGCAAAAGAACG
Found at i:44826823 original size:13 final size:13
Alignment explanation
Indices: 44826805--44826830 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
44826795 CAACATTCAG
44826805 CCGGTGGGAATAA
1 CCGGTGGGAATAA
44826818 CCGGTGGGAATAA
1 CCGGTGGGAATAA
44826831 ACAAATAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.38, T:0.15
Consensus pattern (13 bp):
CCGGTGGGAATAA
Found at i:44827006 original size:45 final size:46
Alignment explanation
Indices: 44826955--44827051 Score: 151
Period size: 45 Copynumber: 2.1 Consensus size: 46
44826945 GAAACGGGAG
* * *
44826955 CGGCGATTTCAGGAGGGAGTGAGAGGGAGAGGGTGGAGGT-GATTT
1 CGGCGATTTCAGGAGGGAGGGAGAGGGAGAGGCTGCAGGTCGATTT
*
44827000 CGGCGATTTCGGGAGGGAGGGAGAGGGAGAGGCTGCAGGTCGATTT
1 CGGCGATTTCAGGAGGGAGGGAGAGGGAGAGGCTGCAGGTCGATTT
44827046 CGGCGA
1 CGGCGA
44827052 GGGTAAAACA
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
45 36 0.77
46 11 0.23
ACGTcount: A:0.21, C:0.11, G:0.51, T:0.18
Consensus pattern (46 bp):
CGGCGATTTCAGGAGGGAGGGAGAGGGAGAGGCTGCAGGTCGATTT
Found at i:44843942 original size:20 final size:20
Alignment explanation
Indices: 44843917--44843954 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
44843907 AACTATCATG
*
44843917 TTTTCTTCATTTTTTTAACC
1 TTTTCTTCATTTTATTAACC
*
44843937 TTTTCTTTATTTTATTAA
1 TTTTCTTCATTTTATTAA
44843955 TAAAATAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.13, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTTCTTCATTTTATTAACC
Found at i:44847166 original size:14 final size:14
Alignment explanation
Indices: 44847121--44847168 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 14
44847111 TTTAAGTAAC
*
44847121 TTAAAATAAATATAT
1 TTAAATTAAATAT-T
*
44847136 TATAAATTATATA-T
1 T-TAAATTAAATATT
44847150 TTAAATTAAATATT
1 TTAAATTAAATATT
44847164 TTAAA
1 TTAAA
44847169 ATAATGAACA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
13 10 0.36
14 8 0.29
15 1 0.04
16 9 0.32
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
TTAAATTAAATATT
Found at i:44847619 original size:10 final size:10
Alignment explanation
Indices: 44847600--44847649 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 10
44847590 TTAGAAATAT
*
44847600 ATTTTTTAAA
1 ATTTTATAAA
44847610 ATTTTATAAA
1 ATTTTATAAA
44847620 ATTTTA-AAA
1 ATTTTATAAA
**
44847629 ACATTATAAA
1 ATTTTATAAA
44847639 CA-TTTATAAA
1 -ATTTTATAAA
44847649 A
1 A
44847650 GTATCAAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
9 8 0.24
10 25 0.74
11 1 0.03
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (10 bp):
ATTTTATAAA
Found at i:44847624 original size:19 final size:20
Alignment explanation
Indices: 44847602--44847649 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 20
44847592 AGAAATATAT
**
44847602 TTTTTAAAATTTTATAAA-A
1 TTTTTAAAACATTATAAACA
*
44847621 TTTTAAAAACATTATAAACA
1 TTTTTAAAACATTATAAACA
*
44847641 TTTATAAAA
1 TTTTTAAAA
44847650 GTATCAAATA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (20 bp):
TTTTTAAAACATTATAAACA
Found at i:44848852 original size:40 final size:40
Alignment explanation
Indices: 44848779--44848871 Score: 134
Period size: 40 Copynumber: 2.3 Consensus size: 40
44848769 TTTGGACCGA
* * *
44848779 AAATGCCGCAAAAGGTAAAGCAGTAGCGGCGTTTTTCTCAT
1 AAATGCCACAAAAGGTAAAGCAATAGCGACGTTTTT-TCAT
44848820 AAATGCCACAAAAGGT-AAGCAATAGCGACGTTTTTTCAT
1 AAATGCCACAAAAGGTAAAGCAATAGCGACGTTTTTTCAT
*
44848859 AAACGCCACAAAA
1 AAATGCCACAAAA
44848872 TATCCTTTTA
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
39 16 0.33
40 17 0.35
41 15 0.31
ACGTcount: A:0.39, C:0.20, G:0.19, T:0.22
Consensus pattern (40 bp):
AAATGCCACAAAAGGTAAAGCAATAGCGACGTTTTTTCAT
Found at i:44848969 original size:32 final size:33
Alignment explanation
Indices: 44848933--44848997 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 33
44848923 TCCCCAAATC
* *
44848933 AATTTCCTAAAATTCCTTATT-TTTCCCCTAAA
1 AATTTCCCAAAATCCCTTATTATTTCCCCTAAA
* *
44848965 AATTTCCCCAAATCCCTTATTATTTTCCCTAAA
1 AATTTCCCAAAATCCCTTATTATTTCCCCTAAA
44848998 TCAAAATCCC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 18 0.64
33 10 0.36
ACGTcount: A:0.31, C:0.28, G:0.00, T:0.42
Consensus pattern (33 bp):
AATTTCCCAAAATCCCTTATTATTTCCCCTAAA
Found at i:44850112 original size:21 final size:18
Alignment explanation
Indices: 44850088--44850133 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
44850078 TAAATTGAGA
44850088 AAATTATTTAATTGGGAAATT
1 AAATTATTT-ATT--GAAATT
*
44850109 AAATTATTTATTTAAATT
1 AAATTATTTATTGAAATT
44850127 AAATTAT
1 AAATTAT
44850134 GATGTTTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 12 0.50
20 3 0.12
21 9 0.38
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.48
Consensus pattern (18 bp):
AAATTATTTATTGAAATT
Found at i:44855025 original size:12 final size:12
Alignment explanation
Indices: 44855008--44855066 Score: 50
Period size: 12 Copynumber: 4.8 Consensus size: 12
44854998 ACTATTTTAC
44855008 TATTTAATTATT-
1 TATTT-ATTATTA
44855020 TATTTATTATTA
1 TATTTATTATTA
*
44855032 TATTATATCATTA
1 TATT-TATTATTA
*
44855045 TGTATTATTA-TA
1 TAT-TTATTATTA
44855057 TTATTTATTA
1 -TATTTATTA
44855067 CTATTGTCAT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
11 6 0.15
12 17 0.44
13 15 0.38
14 1 0.03
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.63
Consensus pattern (12 bp):
TATTTATTATTA
Found at i:44855035 original size:8 final size:8
Alignment explanation
Indices: 44855014--44855066 Score: 53
Period size: 7 Copynumber: 7.1 Consensus size: 8
44855004 TTACTATTTA
44855014 ATTAT-TT
1 ATTATATT
44855021 ATT-TATT
1 ATTATATT
44855028 ATTATATT
1 ATTATATT
44855036 A-TATCATT
1 ATTAT-ATT
*
44855044 A-TGTATT
1 ATTATATT
44855051 ATTATATT
1 ATTATATT
44855059 ATT-TATT
1 ATTATATT
44855066 A
1 A
44855067 CTATTGTCAT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
6 1 0.03
7 20 0.50
8 19 0.47
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (8 bp):
ATTATATT
Found at i:44855037 original size:15 final size:15
Alignment explanation
Indices: 44855019--44855066 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
44855009 ATTTAATTAT
44855019 TTATT-TATTATTATA
1 TTATTATATTATT-TA
*
44855034 TTA-TATCATTATGTA
1 TTATTAT-ATTATTTA
44855049 TTATTATATTATTTA
1 TTATTATATTATTTA
44855064 TTA
1 TTA
44855067 CTATTGTCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
14 1 0.04
15 19 0.68
16 8 0.29
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (15 bp):
TTATTATATTATTTA
Found at i:44855166 original size:2 final size:2
Alignment explanation
Indices: 44855159--44855204 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
44855149 TGTCTTTACA
44855159 AT AT AT AT AT AT 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 AT AT AT AT AT AT
44855201 AT AT
1 AT AT
44855205 CTCGAGCGCG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.