Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 ID=Chr11-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: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1052928 characters in sequence are not A, C, G, or T
File 133 of 210
Found at i:40477669 original size:20 final size:19
Alignment explanation
Indices: 40477619--40477671 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 19
40477609 CTACAAGATA
40477619 AATATTAAATT--TAATTT
1 AATATTAAATTAATAATTT
40477636 AATATTAAGA-TAATCAATTT
1 AATATTAA-ATTAAT-AATTT
40477656 AATATTAAATTAATAA
1 AATATTAAATTAATAA
40477672 AATACTATCA
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
17 9 0.29
18 1 0.03
19 4 0.13
20 17 0.55
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (19 bp):
AATATTAAATTAATAATTT
Found at i:40486423 original size:40 final size:41
Alignment explanation
Indices: 40486339--40486423 Score: 109
Period size: 40 Copynumber: 2.1 Consensus size: 41
40486329 AATTATGGAA
* * * *
40486339 TACTGAATATTGTTTTTGAGTACTGAATTGAATTGTGAAGT
1 TACTGAATATTGTTTATGAGTACTGAATTGAACTCTGAAAT
* *
40486380 TACTGAATATTG-TTATGTGTACTGCATTGAACTCTGAAAT
1 TACTGAATATTGTTTATGAGTACTGAATTGAACTCTGAAAT
40486420 TACT
1 TACT
40486424 AAAGTAATGA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
40 26 0.68
41 12 0.32
ACGTcount: A:0.29, C:0.09, G:0.19, T:0.42
Consensus pattern (41 bp):
TACTGAATATTGTTTATGAGTACTGAATTGAACTCTGAAAT
Found at i:40486727 original size:6 final size:6
Alignment explanation
Indices: 40486716--40486759 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
40486706 GTGTGTTGGA
* * *
40486716 TACTGT TACTGT TACTGT TATTGC TACCGT TACTGAT TACTGT T
1 TACTGT TACTGT TACTGT TACTGT TACTGT TACTG-T TACTGT T
40486760 TAGGTGCTGT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
6 25 0.81
7 6 0.19
ACGTcount: A:0.18, C:0.18, G:0.16, T:0.48
Consensus pattern (6 bp):
TACTGT
Found at i:40494102 original size:40 final size:40
Alignment explanation
Indices: 40494018--40494102 Score: 91
Period size: 40 Copynumber: 2.1 Consensus size: 40
40494008 AATTATGGAA
* * * * *
40494018 TACTGAATATTGTTTTTGAGTACTGAATTGAATTGTGAAGT
1 TACTGAATATTGTTTCT-AGTACCGAATTGAACTCTGAAAT
*
40494059 TACTGAATATTGTTATCT-GTACCGCATTGAACTCTGAAAT
1 TACTGAATATTGTT-TCTAGTACCGAATTGAACTCTGAAAT
40494099 TACT
1 TACT
40494103 ACAGTAATGA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
40 21 0.57
41 14 0.38
42 2 0.05
ACGTcount: A:0.29, C:0.12, G:0.18, T:0.41
Consensus pattern (40 bp):
TACTGAATATTGTTTCTAGTACCGAATTGAACTCTGAAAT
Found at i:40494404 original size:12 final size:12
Alignment explanation
Indices: 40494387--40494430 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
40494377 GTGTGTTGAA
40494387 TACTGTTATTGT
1 TACTGTTATTGT
*
40494399 TACTGTTATTGC
1 TACTGTTATTGT
* *
40494411 TACCGTTACTGAT
1 TACTGTTATTG-T
40494424 TACTGTT
1 TACTGTT
40494431 TAGGTGTTGT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
12 20 0.77
13 6 0.23
ACGTcount: A:0.18, C:0.16, G:0.16, T:0.50
Consensus pattern (12 bp):
TACTGTTATTGT
Found at i:40496872 original size:10 final size:10
Alignment explanation
Indices: 40496857--40496894 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
40496847 GGACTTTCCA
40496857 TGAATGTTCT
1 TGAATGTTCT
40496867 TGAATGTTCT
1 TGAATGTTCT
*
40496877 TAAAATGTTCT
1 T-GAATGTTCT
40496888 TG-ATGTT
1 TGAATGTT
40496895 AAATGCTACA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
9 5 0.20
10 11 0.44
11 9 0.36
ACGTcount: A:0.24, C:0.08, G:0.18, T:0.50
Consensus pattern (10 bp):
TGAATGTTCT
Found at i:40507365 original size:63 final size:63
Alignment explanation
Indices: 40507292--40507434 Score: 164
Period size: 63 Copynumber: 2.3 Consensus size: 63
40507282 AATATCTCTC
* * * *
40507292 ACACAGCCTGGACACACGCCCGTG-TCTCTAGCCCATGTGATTCTAATTCACAAACAATGAGTT
1 ACACGGCCTGGACACACGCCCGTGTTC-CTAGCACATGTGACTCTAATTCAAAAACAATGAGTT
* * * * * * *
40507355 ACATGGCCTGGACACATGCTCGTGTTCCTAGCACGTGTGGCTCTAATTTAAAAACAGTGAGTT
1 ACACGGCCTGGACACACGCCCGTGTTCCTAGCACATGTGACTCTAATTCAAAAACAATGAGTT
40507418 ACACGGCC-GGACACACG
1 ACACGGCCTGGACACACG
40507435 GGCTACCACA
Statistics
Matches: 66, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
62 8 0.12
63 56 0.85
64 2 0.03
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (63 bp):
ACACGGCCTGGACACACGCCCGTGTTCCTAGCACATGTGACTCTAATTCAAAAACAATGAGTT
Found at i:40511892 original size:16 final size:16
Alignment explanation
Indices: 40511871--40511912 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
40511861 GTAAGGAGCA
40511871 TTGCAAAGTGCTCACT
1 TTGCAAAGTGCTCACT
40511887 TTGCAAAGTGCTCACT
1 TTGCAAAGTGCTCACT
*
40511903 TTGCGAAGTG
1 TTGCAAAGTG
40511913 GAAAGAGAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.31
Consensus pattern (16 bp):
TTGCAAAGTGCTCACT
Found at i:40513629 original size:16 final size:16
Alignment explanation
Indices: 40513604--40513635 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
40513594 GTGGTTGCTT
*
40513604 AAAGAGAGAGAGAGAG
1 AAAGAAAGAGAGAGAG
40513620 AAAGAAAGAGAGAGAG
1 AAAGAAAGAGAGAGAG
40513636 GGGTTATTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (16 bp):
AAAGAAAGAGAGAGAG
Found at i:40515256 original size:37 final size:37
Alignment explanation
Indices: 40515197--40515274 Score: 120
Period size: 37 Copynumber: 2.1 Consensus size: 37
40515187 AGTGTTAGAA
* *
40515197 TAATTTAATTTCTATAGAATTAGATTATTAATCTTGT
1 TAATTTAATTTCCATAGAATTAGATTATCAATCTTGT
* *
40515234 TAATTTAATTTCCATAGCATTAGATTATCAATGTTGT
1 TAATTTAATTTCCATAGAATTAGATTATCAATCTTGT
40515271 TAAT
1 TAAT
40515275 GATGTTATGT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.35, C:0.08, G:0.09, T:0.49
Consensus pattern (37 bp):
TAATTTAATTTCCATAGAATTAGATTATCAATCTTGT
Found at i:40525915 original size:21 final size:21
Alignment explanation
Indices: 40525876--40525916 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
40525866 AACTTGGTTA
*
40525876 TATTACCAAAGACCAAGATTG
1 TATTACCAAAGAACAAGATTG
*
40525897 TATTACCAAAGAACGAGATT
1 TATTACCAAAGAACAAGATT
40525917 TTGGGAGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.44, C:0.17, G:0.15, T:0.24
Consensus pattern (21 bp):
TATTACCAAAGAACAAGATTG
Found at i:40526255 original size:62 final size:61
Alignment explanation
Indices: 40526157--40526280 Score: 187
Period size: 62 Copynumber: 2.0 Consensus size: 61
40526147 ACACTATAAA
* * *
40526157 TTCAATTTGATTTTTGTTTTGGTAAATTTATCAACTGAATTATGTTTCATTGACAATTTTAAC
1 TTCAATTTGATTTGTGTTTTGGTAAATTTATCAACTGAATTATG-TT-ATTAACAATGTTAAC
*
40526220 TTCAATTTGATTTGT-TTTTGGTAAATTTATCAACTGAGTTATGTTATTAACAATGTTAAC
1 TTCAATTTGATTTGTGTTTTGGTAAATTTATCAACTGAATTATGTTATTAACAATGTTAAC
40526280 T
1 T
40526281 CTTTTTTCTT
Statistics
Matches: 57, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
60 14 0.25
61 2 0.04
62 27 0.47
63 14 0.25
ACGTcount: A:0.29, C:0.09, G:0.12, T:0.50
Consensus pattern (61 bp):
TTCAATTTGATTTGTGTTTTGGTAAATTTATCAACTGAATTATGTTATTAACAATGTTAAC
Found at i:40527084 original size:15 final size:14
Alignment explanation
Indices: 40527055--40527087 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
40527045 TTCAATAAAC
40527055 TTTT-AAAATTTGA
1 TTTTAAAAATTTGA
40527068 TTTTAAAAATATTGA
1 TTTTAAAAAT-TTGA
40527083 TTTTA
1 TTTTA
40527088 TTTTTTATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 4 0.22
14 5 0.28
15 9 0.50
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (14 bp):
TTTTAAAAATTTGA
Found at i:40527104 original size:17 final size:17
Alignment explanation
Indices: 40527082--40527121 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
40527072 AAAAATATTG
*
40527082 ATTTTATT-TTTTATACA
1 ATTTTATTATTTT-TAAA
40527099 ATTTTATTATTTTTAAA
1 ATTTTATTATTTTTAAA
40527116 ATTTTA
1 ATTTTA
40527122 AATAAGAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (17 bp):
ATTTTATTATTTTTAAA
Found at i:40528619 original size:79 final size:79
Alignment explanation
Indices: 40528514--40528667 Score: 202
Period size: 79 Copynumber: 1.9 Consensus size: 79
40528504 GCGTGTTTAC
* * * *
40528514 TGCAAGTGTTGCCGCGAATATACTATCAAATTTGAATTGTTAAGTTTAAAGTCTATGTTTATTTG
1 TGCAAGTGTTGCCGCGAATATACTATCAAATTTGAATGGTTAAGTTTAAAGTCTATATTTATCTA
40528579 AATAAATTTGTGTG
66 AATAAATTTGTGTG
* * * * * *
40528593 TGCAAGTTTTGCTC-CGAGTATGCTATCATATTTGAATGGTTAATTTTAAAGTTTATATTTATCT
1 TGCAAGTGTTGC-CGCGAATATACTATCAAATTTGAATGGTTAAGTTTAAAGTCTATATTTATCT
40528657 AAATAAATTTG
65 AAATAAATTTG
40528668 CACACTTTCG
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
79 63 0.98
80 1 0.02
ACGTcount: A:0.31, C:0.09, G:0.17, T:0.44
Consensus pattern (79 bp):
TGCAAGTGTTGCCGCGAATATACTATCAAATTTGAATGGTTAAGTTTAAAGTCTATATTTATCTA
AATAAATTTGTGTG
Found at i:40529878 original size:13 final size:13
Alignment explanation
Indices: 40529862--40529886 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40529852 AATTGTAAAA
40529862 AAATAATTATTAT
1 AAATAATTATTAT
40529875 AAATAATTATTA
1 AAATAATTATTA
40529887 AATATTGTTT
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAATAATTATTAT
Found at i:40530030 original size:3 final size:3
Alignment explanation
Indices: 40530024--40530082 Score: 109
Period size: 3 Copynumber: 19.7 Consensus size: 3
40530014 TTCTCCTCCG
*
40530024 CTC CTC CTC CTC CTC CTC CTC CTC CTT CTC CTC CTC CTC CTC CTC CTC
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
40530072 CTC CTC CTC CT
1 CTC CTC CTC CT
40530083 TCTTCAATTG
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.00, C:0.64, G:0.00, T:0.36
Consensus pattern (3 bp):
CTC
Found at i:40530353 original size:17 final size:17
Alignment explanation
Indices: 40530307--40530453 Score: 110
Period size: 18 Copynumber: 8.4 Consensus size: 17
40530297 ATTTTAAAAT
*
40530307 ATTTTTAACAATATTTA
1 ATTTTTTACAATATTTA
40530324 ATAGTTATTTACAATATTTA
1 AT--TT-TTTACAATATTTA
40530344 ATTTTTTACAATATTTA
1 ATTTTTTACAATATTTA
*
40530361 ATTTTTTTACAATTTTTA
1 A-TTTTTTACAATATTTA
40530379 ATATTTTT--AATAATTTAA
1 AT-TTTTTACAAT-ATTT-A
40530397 ATGTTTTTACAAT-TCTTA
1 AT-TTTTTACAATAT-TTA
40530415 TATATTTTTA-AATA-TT-
1 -AT-TTTTTACAATATTTA
* *
40530431 -TTTTTTACTATTTTTA
1 ATTTTTTACAATATTTA
40530447 ATTTTTT
1 ATTTTTT
40530454 TTTACAAATT
Statistics
Matches: 107, Mismatches: 7, Indels: 32
0.73 0.05 0.22
Matches are distributed among these distances:
13 6 0.06
14 3 0.03
15 2 0.02
16 3 0.03
17 28 0.26
18 36 0.34
19 12 0.11
20 17 0.16
ACGTcount: A:0.33, C:0.05, G:0.01, T:0.61
Consensus pattern (17 bp):
ATTTTTTACAATATTTA
Found at i:40530356 original size:37 final size:35
Alignment explanation
Indices: 40530292--40530431 Score: 135
Period size: 37 Copynumber: 3.8 Consensus size: 35
40530282 TAATAACTTG
40530292 TTACAATTTTAAAATATTTTTAACAATATTTAATAGTTAT
1 TTACAATTTT--AATATTTTT-A-AATATTTAATAGTT-T
*
40530332 TTACAATATTTAAT-TTTTTACAATATTTAAT-TTTT
1 TTACAAT-TTTAATATTTTTA-AATATTTAATAGTTT
40530367 TTACAATTTTTAATATTTTT-AATAATTTAA-ATGTTT
1 TTACAA-TTTTAATATTTTTAAAT-ATTTAATA-GTTT
40530403 TTACAATTCTTATATATTTTTAAATATTT
1 TTACAATT-TTA-ATATTTTTAAATATTT
40530432 TTTTTACTAT
Statistics
Matches: 89, Mismatches: 2, Indels: 21
0.79 0.02 0.19
Matches are distributed among these distances:
34 3 0.03
35 21 0.24
36 20 0.22
37 24 0.27
38 8 0.09
39 3 0.03
40 7 0.08
41 3 0.03
ACGTcount: A:0.37, C:0.05, G:0.01, T:0.56
Consensus pattern (35 bp):
TTACAATTTTAATATTTTTAAATATTTAATAGTTT
Found at i:40530384 original size:20 final size:20
Alignment explanation
Indices: 40530241--40530466 Score: 85
Period size: 20 Copynumber: 12.1 Consensus size: 20
40530231 GGTTCACAAA
**
40530241 TTAATATTTTAATA-AATTT
1 TTAATATTTTTTTACAATTT
* * * *
40530260 TAAATAATGTTTTATAATTT
1 TTAATATTTTTTTACAATTT
** *
40530280 TATAATAACTTGTTACAA-TT
1 T-TAATATTTTTTTACAATTT
* * *
40530300 TTAAAATATTTTTAACAATAT
1 TTAATAT-TTTTTTACAATTT
* * *
40530321 TTAATAGTTATTTACAATAT
1 TTAATATTTTTTTACAATTT
*
40530341 TT-A-A-TTTTTTACAATAT
1 TTAATATTTTTTTACAATTT
40530358 TT-A-ATTTTTTTACAATTT
1 TTAATATTTTTTTACAATTT
* *
40530376 TTAATA-TTTTTAATAA--T
1 TTAATATTTTTTTACAATTT
* *
40530393 TTAA-ATGTTTTTACAATTC
1 TTAATATTTTTTTACAATTT
*
40530412 TT-ATATATTTTTA-AA---
1 TTAATATTTTTTTACAATTT
*
40530427 -T-AT-TTTTTTTACTATTT
1 TTAATATTTTTTTACAATTT
*
40530444 TTAATTTTTTTTTACAAATTT
1 TTAATATTTTTTTAC-AATTT
40530465 TT
1 TT
40530467 GGTCTAGTCA
Statistics
Matches: 156, Mismatches: 32, Indels: 36
0.70 0.14 0.16
Matches are distributed among these distances:
13 7 0.04
14 4 0.03
16 1 0.01
17 28 0.18
18 19 0.12
19 35 0.22
20 39 0.25
21 23 0.15
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (20 bp):
TTAATATTTTTTTACAATTT
Found at i:40530385 original size:8 final size:9
Alignment explanation
Indices: 40530304--40530433 Score: 63
Period size: 9 Copynumber: 14.0 Consensus size: 9
40530294 ACAATTTTAA
40530304 AATATTTTT
1 AATATTTTT
* *
40530313 AACAATATTT
1 AA-TATTTTT
40530323 AATAGTTATTT
1 AATA-TT-TTT
*
40530334 ACA-ATATTT
1 A-ATATTTTT
40530343 AAT-TTTTT
1 AATATTTTT
*
40530351 ACA-ATATTT
1 A-ATATTTTT
*
40530360 AATTTTTTT
1 AATATTTTT
40530369 ACA-ATTTTT
1 A-ATATTTTT
40530378 AATATTTTT
1 AATATTTTT
* *
40530387 AATAATTTA
1 AATATTTTT
*
40530396 AATGTTTTT
1 AATATTTTT
*
40530405 ACA-ATTCTT
1 A-ATATTTTT
40530414 ATATATTTTT
1 A-ATATTTTT
40530424 AAATATTTTT
1 -AATATTTTT
40530434 TTTACTATTT
Statistics
Matches: 89, Mismatches: 19, Indels: 25
0.67 0.14 0.19
Matches are distributed among these distances:
8 8 0.09
9 50 0.56
10 24 0.27
11 6 0.07
12 1 0.01
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.58
Consensus pattern (9 bp):
AATATTTTT
Found at i:40530394 original size:10 final size:10
Alignment explanation
Indices: 40530242--40530394 Score: 56
Period size: 10 Copynumber: 15.6 Consensus size: 10
40530232 GTTCACAAAT
40530242 TAATATTTTAA
1 TAAT-TTTTAA
*
40530253 TAAATTTTAAA
1 T-AATTTTTAA
40530264 TAATGTTTT-A
1 TAAT-TTTTAA
40530274 TAATTTTATAA
1 TAATTTT-TAA
*
40530285 TAACTTGTT-A
1 TAA-TTTTTAA
*
40530295 CAA-TTTTAA
1 TAATTTTTAA
*
40530304 AATATTTTTAA
1 TA-ATTTTTAA
* *
40530315 CAATATTTAA
1 TAATTTTTAA
*
40530325 TAGTTATTT-A
1 TAATT-TTTAA
* *
40530335 CAATATTTAA
1 TAATTTTTAA
40530345 T--TTTTT-A
1 TAATTTTTAA
* *
40530352 CAATATTTAA
1 TAATTTTTAA
*
40530362 T--TTTTTTA
1 TAATTTTTAA
*
40530370 CAATTTTTAA
1 TAATTTTTAA
40530380 T-ATTTTTAA
1 TAATTTTTAA
40530389 TAATTT
1 TAATTT
40530395 AAATGTTTTT
Statistics
Matches: 102, Mismatches: 24, Indels: 33
0.64 0.15 0.21
Matches are distributed among these distances:
7 1 0.01
8 12 0.12
9 21 0.21
10 37 0.36
11 25 0.25
12 6 0.06
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.55
Consensus pattern (10 bp):
TAATTTTTAA
Found at i:40532351 original size:51 final size:51
Alignment explanation
Indices: 40532275--40532402 Score: 202
Period size: 51 Copynumber: 2.5 Consensus size: 51
40532265 GACGACGATT
*
40532275 TATGGCATAAGACCATAGATGAAAGAAGCTACGGTAGTCTAGTATAAGGTA
1 TATGGCATAAGACCATAGATGAAAGAAGCTACGGTAGTCTAGTATAAGGCA
* * * *
40532326 TATGGCATAAAACCATAGATGAAAGAGGCTATGGTAGTCTGGTATAAGGCA
1 TATGGCATAAGACCATAGATGAAAGAAGCTACGGTAGTCTAGTATAAGGCA
*
40532377 TATGGCATAAGACCATGGATGAAAGA
1 TATGGCATAAGACCATAGATGAAAGA
40532403 TGTCATGGTA
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 70 1.00
ACGTcount: A:0.39, C:0.12, G:0.27, T:0.23
Consensus pattern (51 bp):
TATGGCATAAGACCATAGATGAAAGAAGCTACGGTAGTCTAGTATAAGGCA
Found at i:40533879 original size:27 final size:28
Alignment explanation
Indices: 40533849--40533975 Score: 127
Period size: 27 Copynumber: 4.7 Consensus size: 28
40533839 AACACGTTAG
*
40533849 GAAAGAAAAACCTTTGTGGC-AAATCAT
1 GAAAGAAAAGCCTTTGTGGCGAAATCAT
*
40533876 GAAAGAAAAGCCTTTGTGACGAAA-CAT
1 GAAAGAAAAGCCTTTGTGGCGAAATCAT
* * *
40533903 AAAAGGAAAGCCTTTGTGGCGAAAT-AC
1 GAAAGAAAAGCCTTTGTGGCGAAATCAT
* * *
40533930 GAAAGAAAAGCCTGTGTGGTG-AATTAT
1 GAAAGAAAAGCCTTTGTGGCGAAATCAT
* * *
40533957 GAAGGGATAGCCTTTGTGG
1 GAAAGAAAAGCCTTTGTGG
40533976 AGAACCTTGT
Statistics
Matches: 82, Mismatches: 15, Indels: 6
0.80 0.15 0.06
Matches are distributed among these distances:
26 3 0.04
27 76 0.93
28 3 0.04
ACGTcount: A:0.39, C:0.13, G:0.27, T:0.22
Consensus pattern (28 bp):
GAAAGAAAAGCCTTTGTGGCGAAATCAT
Found at i:40537779 original size:6 final size:6
Alignment explanation
Indices: 40537762--40537810 Score: 80
Period size: 6 Copynumber: 8.0 Consensus size: 6
40537752 GCAAACGAAT
*
40537762 CATTTC TCATTTT CATTTC CATTTC CATTTC CATTTC CATTTC CATTTC
1 CATTTC -CATTTC CATTTC CATTTC CATTTC CATTTC CATTTC CATTTC
40537811 GAGAAACTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
6 35 0.88
7 5 0.12
ACGTcount: A:0.16, C:0.31, G:0.00, T:0.53
Consensus pattern (6 bp):
CATTTC
Found at i:40540529 original size:19 final size:17
Alignment explanation
Indices: 40540490--40540523 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
40540480 AATTCTTGAG
*
40540490 AAATGATATTTTCATTA
1 AAATAATATTTTCATTA
40540507 AAATAATATTTTCATTA
1 AAATAATATTTTCATTA
40540524 TAAAATTCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (17 bp):
AAATAATATTTTCATTA
Found at i:40543043 original size:45 final size:45
Alignment explanation
Indices: 40542986--40543123 Score: 222
Period size: 45 Copynumber: 3.1 Consensus size: 45
40542976 ATGTTATCAT
*
40542986 CAACATGACGAAAACGAATAAGACCATAGCTGAAAGACGTTATGG
1 CAACATGACGAAAACGAATAAGACCATAGCTGAAAGACGCTATGG
*
40543031 CAACATGACGAAAACGAATAAGACCATAGCTAAAAGACGCTATGG
1 CAACATGACGAAAACGAATAAGACCATAGCTGAAAGACGCTATGG
* * **
40543076 CAACATGACGGAAATGAATAAGACCATATTTGAAAGACGCTATGG
1 CAACATGACGAAAACGAATAAGACCATAGCTGAAAGACGCTATGG
40543121 CAA
1 CAA
40543124 TTTGTCAGAA
Statistics
Matches: 86, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 86 1.00
ACGTcount: A:0.45, C:0.18, G:0.21, T:0.16
Consensus pattern (45 bp):
CAACATGACGAAAACGAATAAGACCATAGCTGAAAGACGCTATGG
Found at i:40543143 original size:45 final size:44
Alignment explanation
Indices: 40542986--40543153 Score: 210
Period size: 45 Copynumber: 3.7 Consensus size: 44
40542976 ATGTTATCAT
*
40542986 CAACATGACGAAAACGAATAAGACCATAGCTGAAAGACGTTATGG
1 CAACATGACG-AAACGAATAAGACCATAGCTGAAAGACGCTATGG
*
40543031 CAACATGACGAAAACGAATAAGACCATAGCTAAAAGACGCTATGG
1 CAACATGACG-AAACGAATAAGACCATAGCTGAAAGACGCTATGG
* **
40543076 CAACATGACGGAAATGAATAAGACCATATTTGAAAGACGCTATGG
1 CAACATGAC-GAAACGAATAAGACCATAGCTGAAAGACGCTATGG
** * * *
40543121 CAATTTGTCAGAAACGAGTAAGACCATGGCTGA
1 CAACATGAC-GAAACGAATAAGACCATAGCTGA
40543154 TAAACAGGAT
Statistics
Matches: 107, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
45 106 0.99
46 1 0.01
ACGTcount: A:0.43, C:0.18, G:0.22, T:0.17
Consensus pattern (44 bp):
CAACATGACGAAACGAATAAGACCATAGCTGAAAGACGCTATGG
Found at i:40543286 original size:66 final size:66
Alignment explanation
Indices: 40543209--40543337 Score: 231
Period size: 66 Copynumber: 2.0 Consensus size: 66
40543199 AGGACGCTAT
* *
40543209 GGCATCCTTTGATAGTTTTTTATCAGGTACTATGTACCGGTGAAGGAGTTCACACCGATGGCTCG
1 GGCATCCTTTGATAGTTATTTATCAGGTACTATGTACCGGTGAAGGAGTTCACACCGAGGGCTCG
40543274 A
66 A
*
40543275 GGCATCCTTTGATAGTTATTTATCAGGTACTATGTACCGGTGAAGGAGTTCATACCGAGGGCT
1 GGCATCCTTTGATAGTTATTTATCAGGTACTATGTACCGGTGAAGGAGTTCACACCGAGGGCT
40543338 TGAGATAGTA
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 60 1.00
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (66 bp):
GGCATCCTTTGATAGTTATTTATCAGGTACTATGTACCGGTGAAGGAGTTCACACCGAGGGCTCG
A
Found at i:40544338 original size:14 final size:14
Alignment explanation
Indices: 40544319--40544345 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
40544309 AAGTTGATTA
40544319 TGAATTGTGGTATT
1 TGAATTGTGGTATT
40544333 TGAATTGTGGTAT
1 TGAATTGTGGTAT
40544346 GTTTTGGCAC
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:0.00, G:0.30, T:0.48
Consensus pattern (14 bp):
TGAATTGTGGTATT
Found at i:40544851 original size:13 final size:13
Alignment explanation
Indices: 40544833--40544890 Score: 50
Period size: 13 Copynumber: 4.5 Consensus size: 13
40544823 TAATGTTTGA
40544833 ATATTTATTTATG
1 ATATTTATTTATG
**
40544846 ATATTTAAAT-TG
1 ATATTTATTTATG
*
40544858 AT-TTT-TTGTTTG
1 ATATTTATT-TATG
40544870 AATATTTATTTATG
1 -ATATTTATTTATG
40544884 ATATTTA
1 ATATTTA
40544891 AATTGATTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 10
0.70 0.10 0.20
Matches are distributed among these distances:
11 4 0.11
12 6 0.17
13 17 0.49
14 6 0.17
15 2 0.06
ACGTcount: A:0.31, C:0.00, G:0.09, T:0.60
Consensus pattern (13 bp):
ATATTTATTTATG
Found at i:40544868 original size:38 final size:38
Alignment explanation
Indices: 40544826--40544902 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
40544816 CTATGAATAA
40544826 TGTTTGAATATTTATTTATGATATTTAAATTGATTTTT
1 TGTTTGAATATTTATTTATGATATTTAAATTGATTTTT
40544864 TGTTTGAATATTTATTTATGATATTTAAATTGATTTTT
1 TGTTTGAATATTTATTTATGATATTTAAATTGATTTTT
40544902 T
1 T
40544903 AACTATTTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.29, C:0.00, G:0.10, T:0.61
Consensus pattern (38 bp):
TGTTTGAATATTTATTTATGATATTTAAATTGATTTTT
Found at i:40549741 original size:29 final size:32
Alignment explanation
Indices: 40549685--40549743 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
40549675 AGTACAAATC
* *
40549685 TAAAATAATAATAATTACTAATTAAATTAATA
1 TAAAATAACAATAATTACAAATTAAATTAATA
40549717 TAAAATAACAATAA-TA-AAATT-AATTAA
1 TAAAATAACAATAATTACAAATTAAATTAA
40549744 CTAAAACTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 6 0.24
30 4 0.16
31 2 0.08
32 13 0.52
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (32 bp):
TAAAATAACAATAATTACAAATTAAATTAATA
Found at i:40549811 original size:29 final size:30
Alignment explanation
Indices: 40549764--40549823 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
40549754 ACCTAAGTTA
*
40549764 AGTTATCGGCTTTGCGAGCTATTCTAGCCT
1 AGTTATCGGCTTTACGAGCTATTCTAGCCT
40549794 AGTT-TCGGCTTTACGAGCTATTCTAGCCT
1 AGTTATCGGCTTTACGAGCTATTCTAGCCT
40549823 A
1 A
40549824 AATCCAGTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 25 0.86
30 4 0.14
ACGTcount: A:0.18, C:0.23, G:0.22, T:0.37
Consensus pattern (30 bp):
AGTTATCGGCTTTACGAGCTATTCTAGCCT
Found at i:40568216 original size:4 final size:4
Alignment explanation
Indices: 40568191--40568232 Score: 57
Period size: 4 Copynumber: 10.0 Consensus size: 4
40568181 TTGAGTATTA
*
40568191 TTAT ATAT TTAAT TTGAT TTAT TTAT TTAT TTAT TTAT TTAT
1 TTAT TTAT TT-AT TT-AT TTAT TTAT TTAT TTAT TTAT TTAT
40568233 AAATAAATCA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
4 26 0.76
5 8 0.24
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (4 bp):
TTAT
Found at i:40568410 original size:19 final size:18
Alignment explanation
Indices: 40568368--40568427 Score: 63
Period size: 19 Copynumber: 3.4 Consensus size: 18
40568358 CCAAACACTA
40568368 AAAAAATAAATCATTTTC
1 AAAAAATAAATCATTTTC
*
40568386 AGAAAAGTAAATCATTTTC
1 A-AAAAATAAATCATTTTC
* *
40568405 TAAAAAT-CAT--TTTTC
1 AAAAAATAAATCATTTTC
40568420 AAAAAATA
1 AAAAAATA
40568428 TTTTACAGGC
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
15 11 0.31
17 2 0.06
18 6 0.17
19 16 0.46
ACGTcount: A:0.53, C:0.10, G:0.03, T:0.33
Consensus pattern (18 bp):
AAAAAATAAATCATTTTC
Found at i:40568413 original size:14 final size:14
Alignment explanation
Indices: 40568394--40568431 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
40568384 TCAGAAAAGT
*
40568394 AAATCATTTTCTAA
1 AAATCATTTTCAAA
40568408 AAATCATTTTTCAAA
1 AAATCA-TTTTCAAA
40568423 AAAT-ATTTT
1 AAATCATTTT
40568432 ACAGGCAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 4 0.18
14 7 0.32
15 11 0.50
ACGTcount: A:0.45, C:0.11, G:0.00, T:0.45
Consensus pattern (14 bp):
AAATCATTTTCAAA
Found at i:40568424 original size:15 final size:15
Alignment explanation
Indices: 40568394--40568431 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
40568384 TCAGAAAAGT
*
40568394 AAATCA-TTTTCTAA
1 AAATCATTTTTCAAA
40568408 AAATCATTTTTCAAA
1 AAATCATTTTTCAAA
40568423 AAAT-ATTTT
1 AAATCATTTT
40568432 ACAGGCAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 11 0.50
15 11 0.50
ACGTcount: A:0.45, C:0.11, G:0.00, T:0.45
Consensus pattern (15 bp):
AAATCATTTTTCAAA
Found at i:40568629 original size:21 final size:21
Alignment explanation
Indices: 40568603--40568658 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
40568593 AACAGCGGTG
*
40568603 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGATACTGTA
*
40568624 GCGGTGAGATTGGATACTGTA
1 GCGGTGAGATTAGATACTGTA
40568645 GCGGTGAGATTAGA
1 GCGGTGAGATTAGA
40568659 AACAATGGTG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.25, C:0.09, G:0.38, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:40569788 original size:16 final size:17
Alignment explanation
Indices: 40569744--40569789 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
40569734 TAAGTTCGAG
40569744 TTTAAATTAAATTTACTA
1 TTTAAA-TAAATTTACTA
40569762 TTTAAAT-AATTTA-TA
1 TTTAAATAAATTTACTA
**
40569777 TTTTTATAAATTT
1 TTTAAATAAATTT
40569790 TAAATAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 7 0.28
16 11 0.44
17 1 0.04
18 6 0.24
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTAAATAAATTTACTA
Found at i:40572101 original size:252 final size:252
Alignment explanation
Indices: 40571645--40572151 Score: 951
Period size: 252 Copynumber: 2.0 Consensus size: 252
40571635 ATGGTACAAA
40571645 TGACTTGTCTGAAATTATGAACTATCTACCTGGGAACAGAACTGCTACTTCTGTTCAAAGGCCAA
1 TGACTTGTCTGAAATTATGAACTATCTACCTGGGAACAGAACTGCTACTTCTGTTCAAAGGCCAA
*
40571710 GTGCAACCACTATTTCATGAAAAAAGCATGCATCGTCCAAAAGATCTTCAAGAATTGAGGACTTG
66 GTGCAACCACTATTTCAGGAAAAAAGCATGCATCGTCCAAAAGATCTTCAAGAATTGAGGACTTG
*
40571775 ATGAAAGTTATTAATAGAGAAAAGAACGATCCAACAGCAGGAGAAATGGCAGGTATTTTGCGTGA
131 ATGAAAGTTATTAATAGAGAAAAGAACGATCCAACAGCAGGAGAAATGGCAGGTATTTTGCATGA
* *
40571840 TAGTTTAGCATCAACTGAATCTTCGAAAGGGAACAAAATAGAGAAGGAAAAAAATAG
196 TACTTTAGCACCAACTGAATCTTCGAAAGGGAACAAAATAGAGAAGGAAAAAAATAG
40571897 TGACTTGTCTGAAATTATGAACTATCTACCTGGGAACAGAACTGCTACTTCTGTTCAAAGGCCAA
1 TGACTTGTCTGAAATTATGAACTATCTACCTGGGAACAGAACTGCTACTTCTGTTCAAAGGCCAA
* *
40571962 GTGCAACCACTATTTCAGGAAAAAAGCATGCATTGTCCAAAAGTTCTTCAAGAATTGAGGACTTG
66 GTGCAACCACTATTTCAGGAAAAAAGCATGCATCGTCCAAAAGATCTTCAAGAATTGAGGACTTG
40572027 ATGAAAGTTATTAATAGAGAAAAGAACGATCCAACAGCAGGAGAAATGGCAGGTATTTTGCATGA
131 ATGAAAGTTATTAATAGAGAAAAGAACGATCCAACAGCAGGAGAAATGGCAGGTATTTTGCATGA
*
40572092 TACTTTAGCACCAACTGAATCTTTGAAAGGGAACAAAATAGAGAAGGAAAAAAATAG
196 TACTTTAGCACCAACTGAATCTTCGAAAGGGAACAAAATAGAGAAGGAAAAAAATAG
40572149 TGA
1 TGA
40572152 TTCAATTGAA
Statistics
Matches: 248, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
252 248 1.00
ACGTcount: A:0.39, C:0.16, G:0.21, T:0.24
Consensus pattern (252 bp):
TGACTTGTCTGAAATTATGAACTATCTACCTGGGAACAGAACTGCTACTTCTGTTCAAAGGCCAA
GTGCAACCACTATTTCAGGAAAAAAGCATGCATCGTCCAAAAGATCTTCAAGAATTGAGGACTTG
ATGAAAGTTATTAATAGAGAAAAGAACGATCCAACAGCAGGAGAAATGGCAGGTATTTTGCATGA
TACTTTAGCACCAACTGAATCTTCGAAAGGGAACAAAATAGAGAAGGAAAAAAATAG
Found at i:40574985 original size:15 final size:15
Alignment explanation
Indices: 40574938--40574977 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
40574928 TATAAGCAAC
40574938 AAAACATAGTAATTA
1 AAAACATAGTAATTA
* *
40574953 AAAAAATAATTAATTA
1 AAAACAT-AGTAATTA
40574969 AAAACATAG
1 AAAACATAG
40574978 CTATTAAATT
Statistics
Matches: 20, Mismatches: 4, Indels: 2
0.77 0.15 0.08
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.65, C:0.05, G:0.05, T:0.25
Consensus pattern (15 bp):
AAAACATAGTAATTA
Found at i:40575195 original size:19 final size:20
Alignment explanation
Indices: 40575171--40575208 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
40575161 TGAGCTGGTT
40575171 GGAGCTGAAA-TGAGCTAAG
1 GGAGCTGAAATTGAGCTAAG
40575190 GGAGCTGAAATTGAGCTAA
1 GGAGCTGAAATTGAGCTAA
40575209 AATCAGCTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.37, C:0.11, G:0.34, T:0.18
Consensus pattern (20 bp):
GGAGCTGAAATTGAGCTAAG
Found at i:40575369 original size:98 final size:98
Alignment explanation
Indices: 40575257--40575452 Score: 392
Period size: 98 Copynumber: 2.0 Consensus size: 98
40575247 TTAGCTCGAG
40575257 CTTCTCCATCATCAATGAGCAGGTCCCTTTGGGAGCTCAATGGAATCAAGAGGTGGGCTTGGTGG
1 CTTCTCCATCATCAATGAGCAGGTCCCTTTGGGAGCTCAATGGAATCAAGAGGTGGGCTTGGTGG
40575322 AGCTTGGGACGTGGTCACGTCAATAAGTATGCT
66 AGCTTGGGACGTGGTCACGTCAATAAGTATGCT
40575355 CTTCTCCATCATCAATGAGCAGGTCCCTTTGGGAGCTCAATGGAATCAAGAGGTGGGCTTGGTGG
1 CTTCTCCATCATCAATGAGCAGGTCCCTTTGGGAGCTCAATGGAATCAAGAGGTGGGCTTGGTGG
40575420 AGCTTGGGACGTGGTCACGTCAATAAGTATGCT
66 AGCTTGGGACGTGGTCACGTCAATAAGTATGCT
40575453 TTTTATCTTT
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
98 98 1.00
ACGTcount: A:0.22, C:0.20, G:0.31, T:0.27
Consensus pattern (98 bp):
CTTCTCCATCATCAATGAGCAGGTCCCTTTGGGAGCTCAATGGAATCAAGAGGTGGGCTTGGTGG
AGCTTGGGACGTGGTCACGTCAATAAGTATGCT
Found at i:40580949 original size:131 final size:130
Alignment explanation
Indices: 40580697--40581020 Score: 350
Period size: 131 Copynumber: 2.5 Consensus size: 130
40580687 CATATATCGC
* * * *
40580697 TAAAATGTGTAACGACCAAACAAGTTGTTGCTAAATGTTAAAATATTTGCAACAATCTTAAATTG
1 TAAAATGTATAACGACAAAACAAGTTGTTGTTAAATGTTAAAATATTAGCAACAATCTTAAATTG
** * * * **
40580762 TCGTTATGTAATTTAATTTTATGCTTATTCATTGCAACGACAAATCATGTTGTTGTGAATT-TGT
66 TCGTTACATAATTTAATTTTATACTTATTAATAGCAACGACAAAT-ATGTCATTGTGAATTAT-T
40580826 AA
129 AA
*
40580828 TAAAATGTATAACGACAAAACAAGTTGTTATTAAATGTTAAAATATTAGCAACAA-CTTTGAAA-
1 TAAAATGTATAACGACAAAACAAGTTGTTGTTAAATGTTAAAATATTAGCAACAATC-TT-AAAT
* * *
40580891 TGTTGTTACATAATTTAATTTTCTACTTATTAATAGCAATGACACAA-ATTGTCATTGTGAATTA
64 TGTCGTTACATAATTTAATTTTATACTTATTAATAGCAACGACA-AATA-TGTCATTGTGAATTA
40580955 TTAA
127 TTAA
* * * ** * * * *
40580959 TAAAATTTACAACGACAAAATAAGTTGTTGTTAAACCTTTAAATACTAGCAGCAACCTTAAA
1 TAAAATGTATAACGACAAAACAAGTTGTTGTTAAATGTTAAAATATTAGCAACAATCTTAAA
40581021 AAAATTGTTA
Statistics
Matches: 163, Mismatches: 24, Indels: 13
0.81 0.12 0.06
Matches are distributed among these distances:
130 5 0.03
131 151 0.93
132 7 0.04
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.36
Consensus pattern (130 bp):
TAAAATGTATAACGACAAAACAAGTTGTTGTTAAATGTTAAAATATTAGCAACAATCTTAAATTG
TCGTTACATAATTTAATTTTATACTTATTAATAGCAACGACAAATATGTCATTGTGAATTATTAA
Found at i:40582523 original size:24 final size:24
Alignment explanation
Indices: 40582489--40582541 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
40582479 TTTCTAGAAG
* **
40582489 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATGAACATAATAT
*
40582513 ATTTAGCATTTATTAACATAATAT
1 ATTTAGCATTTATGAACATAATAT
40582537 ATTTA
1 ATTTA
40582542 ACTTTGATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.49
Consensus pattern (24 bp):
ATTTAGCATTTATGAACATAATAT
Found at i:40582551 original size:24 final size:24
Alignment explanation
Indices: 40582506--40582551 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
40582496 ATTTATGAGT
*
40582506 ATAATATATTTAGCATTTATTAAC
1 ATAATATATTTAACATTTATTAAC
40582530 ATAATATATTTAAC-TTTGATTA
1 ATAATATATTTAACATTT-ATTA
40582552 GAATTAGGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 3 0.15
24 17 0.85
ACGTcount: A:0.41, C:0.07, G:0.04, T:0.48
Consensus pattern (24 bp):
ATAATATATTTAACATTTATTAAC
Found at i:40586936 original size:24 final size:24
Alignment explanation
Indices: 40586873--40586924 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
40586863 TTTCTAGAAG
* * *
40586873 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATTAGCATAATAT
40586897 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATTAGCATAATAT
40586921 ATTT
1 ATTT
40586925 GACTTTGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:40588874 original size:2 final size:2
Alignment explanation
Indices: 40588867--40588894 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
40588857 TCCTATTCCT
40588867 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
40588895 ATGAAAGGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:40593082 original size:24 final size:24
Alignment explanation
Indices: 40593050--40593099 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
40593040 TTTAAGACTT
40593050 AGGTAGTTTTAATATGTTGAATTG
1 AGGTAGTTTTAATATGTTGAATTG
40593074 AGGTAGTTTTAATATGTTGAATTG
1 AGGTAGTTTTAATATGTTGAATTG
40593098 AG
1 AG
40593100 CGTACAGGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.30, C:0.00, G:0.26, T:0.44
Consensus pattern (24 bp):
AGGTAGTTTTAATATGTTGAATTG
Found at i:40602331 original size:45 final size:45
Alignment explanation
Indices: 40602196--40602331 Score: 166
Period size: 45 Copynumber: 3.0 Consensus size: 45
40602186 GTTTGCAAAC
* * * *
40602196 AAGCTGCTAGTATGGTGTGAATAAACCACTCATCGGTGCATATAA
1 AAGCTACTAGTATGTTGTGGATAAACCACTCATCGGTGCAAATAA
** * * * *
40602241 AAGCTACTAGTACATTGTGGATAAACTAGTCATTGGTGCAGATAA
1 AAGCTACTAGTATGTTGTGGATAAACCACTCATCGGTGCAAATAA
40602286 AAGCTACTAGTATGTTGTGGATAAACCACTCATCGGT-CGAAATAA
1 AAGCTACTAGTATGTTGTGGATAAACCACTCATCGGTGC-AAATAA
40602331 A
1 A
40602332 TCACTCATTG
Statistics
Matches: 75, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
44 1 0.01
45 74 0.99
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.27
Consensus pattern (45 bp):
AAGCTACTAGTATGTTGTGGATAAACCACTCATCGGTGCAAATAA
Found at i:40607599 original size:18 final size:18
Alignment explanation
Indices: 40607560--40607599 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
40607550 TAAAAAAATC
*
40607560 ATATTTTTTATATTTAAT
1 ATATTTTTTATATTTAAA
40607578 ATATTTTTTA-ATTTCAAA
1 ATATTTTTTATATTT-AAA
40607596 ATAT
1 ATAT
40607600 GTAGTAACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (18 bp):
ATATTTTTTATATTTAAA
Found at i:40608010 original size:22 final size:22
Alignment explanation
Indices: 40607983--40608042 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
40607973 TACTTAGGTG
40607983 TAAATTAAAATTCATGGGTGTA
1 TAAATTAAAATTCATGGGTGTA
* *
40608005 TAAATT-AAATATCAAGGGTTTA
1 TAAATTAAAAT-TCATGGGTGTA
40608027 TAAATTAAAATT-ATGG
1 TAAATTAAAATTCATGG
40608043 AAATTATGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
21 7 0.21
22 22 0.67
23 4 0.12
ACGTcount: A:0.45, C:0.03, G:0.15, T:0.37
Consensus pattern (22 bp):
TAAATTAAAATTCATGGGTGTA
Found at i:40608947 original size:18 final size:20
Alignment explanation
Indices: 40608915--40608960 Score: 62
Period size: 18 Copynumber: 2.4 Consensus size: 20
40608905 AAAGAGTTAT
40608915 TATTTTTTCATAAATTTTT-
1 TATTTTTTCATAAATTTTTA
40608934 TAATTTTTT-A-AAATTTTTA
1 T-ATTTTTTCATAAATTTTTA
40608953 TATTTTTT
1 TATTTTTT
40608961 GTTTAAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 15 0.60
19 3 0.12
20 7 0.28
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (20 bp):
TATTTTTTCATAAATTTTTA
Found at i:40609435 original size:20 final size:18
Alignment explanation
Indices: 40609400--40609442 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
40609390 ATAACATTGA
40609400 ATTTTGAAATTTTTATAT
1 ATTTTGAAATTTTTATAT
*
40609418 ATTTTGAAATCATTT-TAT
1 ATTTTGAAAT-TTTTATAT
40609436 ATTTTGA
1 ATTTTGA
40609443 TCTTTTTGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 20 0.87
19 3 0.13
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.58
Consensus pattern (18 bp):
ATTTTGAAATTTTTATAT
Found at i:40609750 original size:14 final size:14
Alignment explanation
Indices: 40609733--40609778 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
40609723 TTAATGTCTC
40609733 AAAATTAAAATATA
1 AAAATTAAAATATA
40609747 AAAATTAAAAT-TA
1 AAAATTAAAATATA
* *
40609760 AAATTTCAAAAAATA
1 AAAATT-AAAATATA
40609775 AAAA
1 AAAA
40609779 AATTTAACAG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
13 7 0.26
14 15 0.56
15 5 0.19
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (14 bp):
AAAATTAAAATATA
Found at i:40614484 original size:11 final size:11
Alignment explanation
Indices: 40614462--40614550 Score: 53
Period size: 11 Copynumber: 8.3 Consensus size: 11
40614452 ATATATACTA
*
40614462 AATAGAATAAT
1 AATAAAATAAT
40614473 AATAATAA-AAT
1 AATAA-AATAAT
40614484 AATAAAAT-AT
1 AATAAAATAAT
* *
40614494 CATTTAAA-AAT
1 -AATAAAATAAT
*
40614505 -A-AAAATAAA
1 AATAAAATAAT
*
40614514 AATAAAAATAAA
1 AAT-AAAATAAT
*
40614526 AATAAAATATT
1 AATAAAATAAT
*
40614537 AATAAACTAAT
1 AATAAAATAAT
40614548 AAT
1 AAT
40614551 TAATTAATTA
Statistics
Matches: 60, Mismatches: 10, Indels: 16
0.70 0.12 0.19
Matches are distributed among these distances:
8 3 0.05
9 2 0.03
10 5 0.08
11 37 0.62
12 13 0.22
ACGTcount: A:0.70, C:0.02, G:0.01, T:0.27
Consensus pattern (11 bp):
AATAAAATAAT
Found at i:40614513 original size:12 final size:12
Alignment explanation
Indices: 40614498--40614532 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
40614488 AAATATCATT
40614498 TAAAAATAAAAA
1 TAAAAATAAAAA
40614510 TAAAAATAAAAA
1 TAAAAATAAAAA
40614522 TAAAAATAAAA
1 TAAAAATAAAA
40614533 TATTAATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (12 bp):
TAAAAATAAAAA
Found at i:40614519 original size:18 final size:18
Alignment explanation
Indices: 40614498--40614532 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
40614488 AAATATCATT
40614498 TAAAAATAAAAATAAAAA
1 TAAAAATAAAAATAAAAA
40614516 TAAAAATAAAAATAAAA
1 TAAAAATAAAAATAAAA
40614533 TATTAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (18 bp):
TAAAAATAAAAATAAAAA
Found at i:40615021 original size:23 final size:23
Alignment explanation
Indices: 40614990--40615040 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
40614980 ACCTACTTTC
* * *
40614990 TTACTGTAGTAATTTTCGGGGTA
1 TTACAGTAGTAATTTTCAGGATA
40615013 TTACAGTAGTAATTTTCAGGATA
1 TTACAGTAGTAATTTTCAGGATA
40615036 TTACA
1 TTACA
40615041 ATATAGATGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.29, C:0.10, G:0.20, T:0.41
Consensus pattern (23 bp):
TTACAGTAGTAATTTTCAGGATA
Found at i:40617683 original size:29 final size:29
Alignment explanation
Indices: 40617644--40617701 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
40617634 TTTAATAATA
40617644 AAAATGAATAAACTTTTAAAAGGAAAAAT
1 AAAATGAATAAACTTTTAAAAGGAAAAAT
40617673 AAAATGAATAAACTTTTAAAAGGAAAAAT
1 AAAATGAATAAACTTTTAAAAGGAAAAAT
40617702 TTAATTTACT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.62, C:0.03, G:0.10, T:0.24
Consensus pattern (29 bp):
AAAATGAATAAACTTTTAAAAGGAAAAAT
Found at i:40622673 original size:17 final size:17
Alignment explanation
Indices: 40622631--40622666 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
40622621 CATATATATA
40622631 TAAAAAAATAATTACAT
1 TAAAAAAATAATTACAT
40622648 TAAAAAAATAATTACAT
1 TAAAAAAATAATTACAT
40622665 TA
1 TA
40622667 TGGAAATCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.31
Consensus pattern (17 bp):
TAAAAAAATAATTACAT
Found at i:40624390 original size:45 final size:44
Alignment explanation
Indices: 40624268--40624564 Score: 245
Period size: 44 Copynumber: 6.7 Consensus size: 44
40624258 ATCCAAGATT
* * *
40624268 TTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTAT-CGA-C
1 TTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATT-TGCCATC
*
40624311 TTTAATTTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATC
1 -TTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATC
* * *
40624356 TTCAATCTGC-CTCATTGCAACTTCA-GGAGGATAAGACTTG-CTTAC
1 TT-AATCTGCTC-CACTGCAACTTCAGGGA-GATAAGATTTGCCAT-C
* * *
40624401 TTAGTCTGCTCCACTGCAACTTCAGGGAGATAGGATTATCGGC-T-
1 TTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATT-T-GCCATC
*
40624445 TTAATCTGCTCCACTGCAACTTTAGGGAGATAAGATTTGCCATC
1 TTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATC
* * * *
40624489 TTCAGTCTGC-CTCACTACAACTTCA-GGAGGATAAGACTTG-CTTAC
1 TT-AATCTGCTC-CACTGCAACTTCAGGGA-GATAAGATTTGCCAT-C
* * * *
40624534 TTAGTTTGCTCCACTACAACTTTAGGGAGAT
1 TTAATCTGCTCCACTGCAACTTCAGGGAGAT
40624565 CAAACTAGAT
Statistics
Matches: 211, Mismatches: 23, Indels: 38
0.78 0.08 0.14
Matches are distributed among these distances:
42 2 0.01
43 3 0.01
44 132 0.63
45 71 0.34
46 2 0.01
47 1 0.00
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.31
Consensus pattern (44 bp):
TTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATC
Found at i:40624422 original size:133 final size:133
Alignment explanation
Indices: 40624275--40624564 Score: 499
Period size: 133 Copynumber: 2.2 Consensus size: 133
40624265 ATTTTAATCC
*
40624275 GCTCCACTGCAACTTCAGGGAGATAGGATTATCGACTTTAATTTGCTCCACTGCAACTTCAGGGA
1 GCTCCACTGCAACTTCAGGGAGATAGGATTATCGACTTTAATCTGCTCCACTGCAACTTCAGGGA
* *
40624340 GATAAGATTTGCCATCTTCAATCTGCCTCATTGCAACTTCAGGAGGATAAGACTTGCTTACTTAG
66 GATAAGATTTGCCATCTTCAATCTGCCTCACTACAACTTCAGGAGGATAAGACTTGCTTACTTAG
40624405 TCT
131 TCT
* *
40624408 GCTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTTAATCTGCTCCACTGCAACTTTAGGGA
1 GCTCCACTGCAACTTCAGGGAGATAGGATTATCGACTTTAATCTGCTCCACTGCAACTTCAGGGA
*
40624473 GATAAGATTTGCCATCTTCAGTCTGCCTCACTACAACTTCAGGAGGATAAGACTTGCTTACTTAG
66 GATAAGATTTGCCATCTTCAATCTGCCTCACTACAACTTCAGGAGGATAAGACTTGCTTACTTAG
*
40624538 TTT
131 TCT
* *
40624541 GCTCCACTACAACTTTAGGGAGAT
1 GCTCCACTGCAACTTCAGGGAGAT
40624565 CAAACTAGAT
Statistics
Matches: 148, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
133 148 1.00
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.30
Consensus pattern (133 bp):
GCTCCACTGCAACTTCAGGGAGATAGGATTATCGACTTTAATCTGCTCCACTGCAACTTCAGGGA
GATAAGATTTGCCATCTTCAATCTGCCTCACTACAACTTCAGGAGGATAAGACTTGCTTACTTAG
TCT
Found at i:40624496 original size:89 final size:87
Alignment explanation
Indices: 40624267--40624564 Score: 252
Period size: 89 Copynumber: 3.4 Consensus size: 87
40624257 GATCCAAGAT
* * * * *
40624267 TTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTAT-CGA-CTTTAATTTGCTCCACTGCA
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATT-TGCCATC-TTAGTCTGCTCCACTGCA
40624330 ACTTCAGGGAGATAAGATTTGCCA
64 ACTTCAGGGAGATAAGATTTGCCA
* * *
40624354 TCTTCAATCTGC-CTCATTGCAACTTCA-GGAGGATAAGACTTG-CTTACTTAGTCTGCTCCACT
1 T-TT-AATCTGCTC-CACTGCAACTTCAGGGA-GATAAGATTTGCCAT-CTTAGTCTGCTCCACT
* *
40624416 GCAACTTCAGGGAGATAGGATTATCGGC-
61 GCAACTTCAGGGAGATAAGATT-T-GCCA
* *
40624444 TTTAATCTGCTCCACTGCAACTTTAGGGAGATAAGATTTGCCATCTTCAGTCTGC-CTCACTACA
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTT-AGTCTGCTC-CACTGCA
* *
40624508 ACTTCA-GGAGGATAAGACTTGCTTA
64 ACTTCAGGGA-GATAAGATTTGC-CA
* * * * *
40624533 CTTAGTTTGCTCCACTACAACTTTAGGGAGAT
1 TTTAATCTGCTCCACTGCAACTTCAGGGAGAT
40624565 CAAACTAGAT
Statistics
Matches: 171, Mismatches: 23, Indels: 32
0.76 0.10 0.14
Matches are distributed among these distances:
87 2 0.01
88 43 0.25
89 121 0.71
90 3 0.02
91 2 0.01
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.31
Consensus pattern (87 bp):
TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTAGTCTGCTCCACTGCAAC
TTCAGGGAGATAAGATTTGCCA
Found at i:40637025 original size:21 final size:19
Alignment explanation
Indices: 40636999--40637086 Score: 60
Period size: 21 Copynumber: 4.6 Consensus size: 19
40636989 AAACATTCGT
40636999 TAAAAAAAATAAATATGTACA
1 TAAAAAAAATAAATA--TACA
* *
40637020 TAAAAACAACAAATATACA
1 TAAAAAAAATAAATATACA
40637039 TAGATAAATAAATAAATA-A-A
1 TA-A-AAA-AAATAAATATACA
*
40637059 T-AAATAAAT-AAT-TACA
1 TAAAAAAAATAAATATACA
*
40637075 TTAAAAAAATAA
1 TAAAAAAAATAA
40637087 TTACATTATG
Statistics
Matches: 54, Mismatches: 6, Indels: 17
0.70 0.08 0.22
Matches are distributed among these distances:
15 4 0.07
16 6 0.11
17 9 0.17
18 2 0.04
19 6 0.11
20 3 0.06
21 17 0.31
22 7 0.13
ACGTcount: A:0.68, C:0.06, G:0.02, T:0.24
Consensus pattern (19 bp):
TAAAAAAAATAAATATACA
Found at i:40637051 original size:4 final size:4
Alignment explanation
Indices: 40637042--40637069 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
40637032 ATATACATAG
40637042 ATAA ATAA ATAA ATAA ATAA ATAA ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA
40637070 TTACATTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAA
Found at i:40637101 original size:17 final size:17
Alignment explanation
Indices: 40637059--40637094 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
40637049 AATAAATAAA
*
40637059 TAAATAAATAATTACAT
1 TAAAAAAATAATTACAT
40637076 TAAAAAAATAATTACAT
1 TAAAAAAATAATTACAT
40637093 TA
1 TA
40637095 TGGAAATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (17 bp):
TAAAAAAATAATTACAT
Found at i:40639217 original size:146 final size:146
Alignment explanation
Indices: 40638950--40639237 Score: 522
Period size: 146 Copynumber: 2.0 Consensus size: 146
40638940 CATGACATGT
40638950 TGGAACGCAGTCTAATAGCAGCTTAGATTAACTAAATACTTTCGGCAAGATTCAAAGTTCTATAG
1 TGGAACGCAGTCTAATAGCAGCTTAGATTAACTAAATACTTTCGGCAAGATTCAAAGTTCTATAG
* *
40639015 TTAGATTAAAAATATTATCTGAGTGTATATCCTTTTGTTATTAAATTTTATATTTTCAATTATTA
66 TTAGATTAAAAACATTAACTGAGTGTATATCCTTTTGTTATTAAATTTTATATTTTCAATTATTA
40639080 AACCCTCAAATCATAG
131 AACCCTCAAATCATAG
* *
40639096 TGGAACGCAGTCTAATCGCAGCTTAGATTAACTAAATACTTTCGGCAAGATTCAAAGTTCTATAT
1 TGGAACGCAGTCTAATAGCAGCTTAGATTAACTAAATACTTTCGGCAAGATTCAAAGTTCTATAG
* *
40639161 TTAGATTAAAAACATTAACTGAGTGTATATCCTTTTGTTATTAAGTTTTATTTTTTCAATTATTA
66 TTAGATTAAAAACATTAACTGAGTGTATATCCTTTTGTTATTAAATTTTATATTTTCAATTATTA
40639226 AACCCTCAAATC
131 AACCCTCAAATC
40639238 TTAGGTATCT
Statistics
Matches: 136, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
146 136 1.00
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.39
Consensus pattern (146 bp):
TGGAACGCAGTCTAATAGCAGCTTAGATTAACTAAATACTTTCGGCAAGATTCAAAGTTCTATAG
TTAGATTAAAAACATTAACTGAGTGTATATCCTTTTGTTATTAAATTTTATATTTTCAATTATTA
AACCCTCAAATCATAG
Found at i:40647550 original size:20 final size:17
Alignment explanation
Indices: 40647507--40647552 Score: 74
Period size: 17 Copynumber: 2.6 Consensus size: 17
40647497 ATTTAGATTG
40647507 AACACAAATTATGGAAC
1 AACACAAATTATGGAAC
40647524 AACACAAATTATGGAAC
1 AACACAAATTATGGAAC
40647541 AATCACACAATT
1 AA-CACA-AATT
40647553 TTAGCATACC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 19 0.70
18 4 0.15
19 4 0.15
ACGTcount: A:0.52, C:0.20, G:0.09, T:0.20
Consensus pattern (17 bp):
AACACAAATTATGGAAC
Found at i:40651164 original size:102 final size:102
Alignment explanation
Indices: 40650988--40651331 Score: 462
Period size: 102 Copynumber: 3.4 Consensus size: 102
40650978 TATCGATGAA
* * * * *
40650988 CACGTGTGTAGTATTGTGTAAAGGCTACTACGTGTATCTATAAATGATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
*
40651053 TAAGTGAAGGCTACAATGTGTACC-AAGAAGCTTTGGT
66 TAAGTGAAGGCTACTATGTGTACCGAA-AAGCTTTGGT
*
40651090 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
40651155 TAAGTGAAGGCTACTATGTGTACCGAAAAGCTTTGGT
66 TAAGTGAAGGCTACTATGTGTACCGAAAAGCTTTGGT
* * * *** * *
40651192 TACGTGTGTAGTACTATGTGAAGGCTACTATGTGAACCG-TAAAACTTGATCACGTGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
* * * *
40651256 TATGTGAAGGCTACTACGTGAACCGTAAAA-C-TTGAT
66 TAAGTGAAGGCTACTATGTGTACCG-AAAAGCTTTGGT
*
40651292 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGA
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGA
40651332 ATGATAAAAG
Statistics
Matches: 217, Mismatches: 22, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
100 39 0.18
101 43 0.20
102 133 0.61
103 2 0.01
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (102 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
TAAGTGAAGGCTACTATGTGTACCGAAAAGCTTTGGT
Found at i:40651322 original size:50 final size:50
Alignment explanation
Indices: 40650988--40651325 Score: 353
Period size: 51 Copynumber: 6.7 Consensus size: 50
40650978 TATCGATGAA
* * * * *
40650988 CACGTGTGTAGTATTGTGTAAAGGCTACTACGTGTATC-TATAAA-TGATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTA-AAACT--TGGT
* * * * *
40651039 CACATGTGTAGTACTAAGTGAAGGCTACAATGTGTACC--AAGAAGCTTTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAA-AA-C-TTGGT
* * ***
40651090 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCG-TAAAACTTGGT
* * * *
40651141 CACATGTGTAGTACTAAGTGAAGGCTACTATGTGTACCG-AAAAGCTTTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAA-C-TTGGT
* * *
40651192 TACGTGTGTAGTACTATGTGAAGGCTACTATGTGAACCGTAAAACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGGT
*
40651242 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGGT
40651292 CACGTGTGTAGTACTATGTGAAGGCTACTACGTG
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTG
40651326 TATCGAATGA
Statistics
Matches: 243, Mismatches: 34, Indels: 21
0.82 0.11 0.07
Matches are distributed among these distances:
49 4 0.02
50 89 0.37
51 142 0.58
52 4 0.02
53 2 0.01
54 2 0.01
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (50 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGGT
Found at i:40658898 original size:51 final size:49
Alignment explanation
Indices: 40658812--40659156 Score: 352
Period size: 51 Copynumber: 6.8 Consensus size: 49
40658802 TATCGATGAA
* * *
40658812 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAACTGATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGAAAACT--TGAT
* * * * * *
40658863 CACATGTGTAGTACTAAGTGAAGGCTACAATGTGTA-CTGAGAAGCTTTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATC-GA-AAAC-TTGAT
* * *
40658914 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATC-AATAAATGATGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGAA-AACT--TGAT
* * * * * *
40658965 CACATGTGCAGTACTAAGTGAAGGCTACTATGTGTACCGAAAAGCTTTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGAAAA-C-TTGAT
* * * * *
40659016 TACGTGTGTAGTACTATGTGAAGGCTACTATGTGAACCGTAAAACTTGAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCG-AAAACTTGAT
*
40659066 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGTAAAACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCG-AAAACTTGAT
40659116 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGAA
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGAA
40659157 TGATAAAAGT
Statistics
Matches: 246, Mismatches: 37, Indels: 24
0.80 0.12 0.08
Matches are distributed among these distances:
49 4 0.02
50 90 0.37
51 141 0.57
52 9 0.04
53 2 0.01
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.30
Consensus pattern (49 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGAAAACTTGAT
Found at i:40658988 original size:102 final size:101
Alignment explanation
Indices: 40658812--40659149 Score: 412
Period size: 102 Copynumber: 3.3 Consensus size: 101
40658802 TATCGATGAA
* * * * *
40658812 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAACTGATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCAATAAATGATGATCACATGTGTAGTAC
*
40658877 TAAGTGAAGGCTACAATGTGTACTGAGAAGCTTTGGT
66 TAAGTGAAGGCTACTATGTGTACTGA-AAGCTTTGGT
* *
40658914 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCAATAAATGATGATCACATGTGCAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCAATAAATGATGATCACATGTGTAGTAC
*
40658979 TAAGTGAAGGCTACTATGTGTACCGAAAAGCTTTGGT
66 TAAGTGAAGGCTACTATGTGTACTG-AAAGCTTTGGT
* * ** *** * *
40659016 TACGTGTGTAGTACTATGTGAAGGCTACTATGTGAA-CCGTAAAACTTGACCACGTGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCAATAAATGATGATCACATGTGTAGTAC
* * * * *
40659080 TATGTGAAGGCTACTACGTG-AATCGTAAAAC-TTGAT
66 TAAGTGAAGGCTACTATGTGTACT-G-AAAGCTTTGGT
40659116 CACGTGTGTAGTACTATGTGAAGGCTACTACGTG
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTG
40659150 TATCGAATGA
Statistics
Matches: 207, Mismatches: 27, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
100 37 0.18
101 43 0.21
102 126 0.61
103 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (101 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCAATAAATGATGATCACATGTGTAGTAC
TAAGTGAAGGCTACTATGTGTACTGAAAGCTTTGGT
Found at i:40660415 original size:2 final size:2
Alignment explanation
Indices: 40660408--40660441 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
40660398 ATTTTTGTAA
40660408 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
40660442 TTCATATCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40677579 original size:68 final size:68
Alignment explanation
Indices: 40677440--40677570 Score: 181
Period size: 68 Copynumber: 1.9 Consensus size: 68
40677430 GAAGTTTGCC
* * * *
40677440 AGGACAGTAAACATGACACTATATTATATAAAATCATAACTGGGATATGGAAACATTTGAAGTCT
1 AGGACAGTAAACATGACACCATATTATATAAAACCATAACTAGGATATGAAAACATTTGAAGTCT
40677505 ACT
66 ACT
* * * * *
40677508 AGGACAGTAAACATGACACCATATTGTGTAAGACCATAGCTAGGCTATGAAAACATTTGAAGT
1 AGGACAGTAAACATGACACCATATTATATAAAACCATAACTAGGATATGAAAACATTTGAAGT
40677571 TCATTAGGAT
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
68 54 1.00
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.26
Consensus pattern (68 bp):
AGGACAGTAAACATGACACCATATTATATAAAACCATAACTAGGATATGAAAACATTTGAAGTCT
ACT
Found at i:40680110 original size:43 final size:43
Alignment explanation
Indices: 40680049--40680132 Score: 168
Period size: 43 Copynumber: 2.0 Consensus size: 43
40680039 AAATTCAAAG
40680049 GGATAAGAACAAGAGTTCAAATGTTTGAATTTCAAACGTTTTT
1 GGATAAGAACAAGAGTTCAAATGTTTGAATTTCAAACGTTTTT
40680092 GGATAAGAACAAGAGTTCAAATGTTTGAATTTCAAACGTTT
1 GGATAAGAACAAGAGTTCAAATGTTTGAATTTCAAACGTTT
40680133 CACACATATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (43 bp):
GGATAAGAACAAGAGTTCAAATGTTTGAATTTCAAACGTTTTT
Found at i:40680741 original size:37 final size:35
Alignment explanation
Indices: 40680691--40680783 Score: 105
Period size: 36 Copynumber: 2.5 Consensus size: 35
40680681 GAAAACAAAC
* * *
40680691 AAAAAAAATAAAAAAATTATATATTGATCAAAGTTTA
1 AAAAAAAACAAAAAAATT-TAGAAT-ATCAAAGTTTA
*
40680728 AAAAAAAACAAAAAAAATTTCGAATATCAAAGTTTA
1 AAAAAAAAC-AAAAAAATTTAGAATATCAAAGTTTA
*
40680764 AAAGAAAAAGAAAAAAATTT
1 AAA-AAAAACAAAAAAATTT
40680784 CGAAAAATAT
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
36 24 0.49
37 16 0.33
38 9 0.18
ACGTcount: A:0.66, C:0.04, G:0.06, T:0.24
Consensus pattern (35 bp):
AAAAAAAACAAAAAAATTTAGAATATCAAAGTTTA
Found at i:40680757 original size:36 final size:36
Alignment explanation
Indices: 40680717--40680787 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
40680707 TTATATATTG
40680717 ATCAAAGTTTAAAA-AAAAACAAAAAAAATTTCGAAT
1 ATCAAAGTTTAAAAGAAAAA-AAAAAAAATTTCGAAT
*
40680753 ATCAAAGTTTAAAAGAAAAAGAAAAAAATTTCGAA
1 ATCAAAGTTTAAAAGAAAAAAAAAAAAATTTCGAA
40680788 AAATATATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
36 28 0.85
37 5 0.15
ACGTcount: A:0.63, C:0.07, G:0.08, T:0.21
Consensus pattern (36 bp):
ATCAAAGTTTAAAAGAAAAAAAAAAAAATTTCGAAT
Found at i:40686572 original size:42 final size:42
Alignment explanation
Indices: 40686513--40686595 Score: 157
Period size: 42 Copynumber: 2.0 Consensus size: 42
40686503 AAATTCAAAG
*
40686513 GGATAAGAACAAGAGTTCAAATGTTTGAATTTCAAACGTTTT
1 GGATAACAACAAGAGTTCAAATGTTTGAATTTCAAACGTTTT
40686555 GGATAACAACAAGAGTTCAAATGTTTGAATTTCAAACGTTT
1 GGATAACAACAAGAGTTCAAATGTTTGAATTTCAAACGTTT
40686596 CACACATATT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.33
Consensus pattern (42 bp):
GGATAACAACAAGAGTTCAAATGTTTGAATTTCAAACGTTTT
Found at i:40687659 original size:20 final size:21
Alignment explanation
Indices: 40687636--40687675 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
40687626 ATATCATCGT
*
40687636 TCATATCAAAAATAA-TAAAC
1 TCATAGCAAAAATAAGTAAAC
*
40687656 TCATAGCAAACATAAGTAAA
1 TCATAGCAAAAATAAGTAAA
40687676 TTAAATAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.57, C:0.15, G:0.05, T:0.23
Consensus pattern (21 bp):
TCATAGCAAAAATAAGTAAAC
Found at i:40695616 original size:17 final size:17
Alignment explanation
Indices: 40695594--40695626 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
40695584 ATGAATGAAA
40695594 AAATGCTAG-GGCAATTG
1 AAATGCT-GTGGCAATTG
40695611 AAATGCTGTGGCAATT
1 AAATGCTGTGGCAATT
40695627 CTCAAAGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 1 0.07
17 14 0.93
ACGTcount: A:0.33, C:0.12, G:0.27, T:0.27
Consensus pattern (17 bp):
AAATGCTGTGGCAATTG
Found at i:40700071 original size:22 final size:22
Alignment explanation
Indices: 40700045--40700095 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
40700035 AGAGTGAATA
40700045 AGTACGTGAAACATGAGAGCTT
1 AGTACGTGAAACATGAGAGCTT
* **
40700067 AGTACGTTAGCCATGAGAGCTT
1 AGTACGTGAAACATGAGAGCTT
40700089 AGTACGT
1 AGTACGT
40700096 TAGCCATGAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.31, C:0.16, G:0.27, T:0.25
Consensus pattern (22 bp):
AGTACGTGAAACATGAGAGCTT
Found at i:40700096 original size:22 final size:22
Alignment explanation
Indices: 40700056--40700120 Score: 103
Period size: 22 Copynumber: 3.0 Consensus size: 22
40700046 GTACGTGAAA
40700056 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
40700078 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
* * *
40700100 CATGAGGGTTTAGTTCGTTAG
1 CATGAGAGCTTAGTACGTTAG
40700121 ATATTTGAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.25, C:0.15, G:0.29, T:0.31
Consensus pattern (22 bp):
CATGAGAGCTTAGTACGTTAGC
Found at i:40700658 original size:30 final size:30
Alignment explanation
Indices: 40700624--40700683 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
40700614 ACAATAAAGT
40700624 ATATGAATGAATTGTGTATAATTGGTTATA
1 ATATGAATGAATTGTGTATAATTGGTTATA
40700654 ATATGAATGAATTGTGTATAATTGGTTATA
1 ATATGAATGAATTGTGTATAATTGGTTATA
40700684 TGCCTGATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.37, C:0.00, G:0.20, T:0.43
Consensus pattern (30 bp):
ATATGAATGAATTGTGTATAATTGGTTATA
Found at i:40705891 original size:34 final size:34
Alignment explanation
Indices: 40705848--40705916 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
40705838 TAAGCTTACC
40705848 AGGAGGTTGTATATGACTATCATGCCATCTCTTT
1 AGGAGGTTGTATATGACTATCATGCCATCTCTTT
40705882 AGGAGGTTGTATATGACTATCATGCCATCTCTTT
1 AGGAGGTTGTATATGACTATCATGCCATCTCTTT
40705916 A
1 A
40705917 ATCTTTCTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.38
Consensus pattern (34 bp):
AGGAGGTTGTATATGACTATCATGCCATCTCTTT
Found at i:40717435 original size:26 final size:26
Alignment explanation
Indices: 40717406--40717456 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
40717396 GTAATTCTAG
40717406 AATATCATAACATATATCAGTTTCAA
1 AATATCATAACATATATCAGTTTCAA
* *
40717432 AATATCATAGCATGTATCAGTTTCA
1 AATATCATAACATATATCAGTTTCA
40717457 GAACACTTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.41, C:0.16, G:0.08, T:0.35
Consensus pattern (26 bp):
AATATCATAACATATATCAGTTTCAA
Found at i:40719060 original size:19 final size:19
Alignment explanation
Indices: 40719036--40719073 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
40719026 TTTTCTTACT
40719036 AAAAATTATTTATCTCTTA
1 AAAAATTATTTATCTCTTA
40719055 AAAAATTATTTATCTCTTA
1 AAAAATTATTTATCTCTTA
40719074 GTACGAAATT
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:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (19 bp):
AAAAATTATTTATCTCTTA
Found at i:40719489 original size:9 final size:9
Alignment explanation
Indices: 40719470--40719504 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
40719460 TTTTTGCATC
40719470 ATTTACTCTT
1 ATTT-CTCTT
40719480 ATTTCTCTT
1 ATTTCTCTT
*
40719489 ATTTCTCAT
1 ATTTCTCTT
40719498 ATTTCTC
1 ATTTCTC
40719505 GATAGCAAGC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 20 0.83
10 4 0.17
ACGTcount: A:0.17, C:0.23, G:0.00, T:0.60
Consensus pattern (9 bp):
ATTTCTCTT
Found at i:40723702 original size:338 final size:338
Alignment explanation
Indices: 40723086--40724003 Score: 1435
Period size: 338 Copynumber: 2.7 Consensus size: 338
40723076 CCCTGTTTCC
* * *
40723086 ACCCTTCCACAAACTTGTAATAGTATTCTACTAACCACATAAAGCTTTGCACCTTAGTAACACTT
1 ACCCTTCCACAAACTTGCAATAGTATTCTACTAACCTCATAAAGCTTTGCACCTCAGTAACACTT
* * * * **
40723151 TTTGGTCATTTCCACTCTAAAACTTCCTCAATCCTCTTTGGGTCTATGCAAATTCCCTCAACAAA
66 TTTGGTCATTTCCACTCTAAAATTTCCTCAATCTTCTTTGGGTCTACGCAAAATCCCTCCGCAAA
*
40723216 ATCCACATAACACAAGAATGCTACCTCCCTTAACCAAAATTCACACTTCCTGAGCTTCACGAATA
131 ATCCACATAACCCAAGAATGCTACCTCCCTTAACCAAAATTCACACTTCCTGAGCTTCACGAATA
* * * *
40723281 GTTGCTTCTCTCATAAAATATGTAACACGGTTTCCAGGTGAGCATCACCTTAAGTCTTTCAAAGC
196 GTTGCTTCTCTCGTAAAATATGTAACACAGTTTGCAGGTGAGCATCACCTTAAGTCTTTAAAAGC
* *
40723346 TTTCTTGACTTTCCTCTATCCATTCGAACTCCACATCTTTCTGA-AGTAGCTTTATTATGGGTGT
261 TTTCTTGACTTTCCTCTATCCATGCGAACTCCACATCTTTCT-ACAGTAGATTTATTATGGGTGT
40723410 CGCAATGGTGGCGA
325 CGCAATGGTGGCGA
*
40723424 ACCCTTCTACAAACTTGCAATAGTATTCTACTAACCTCATAAAGCTTTGCACCTCAGTAACACTT
1 ACCCTTCCACAAACTTGCAATAGTATTCTACTAACCTCATAAAGCTTTGCACCTCAGTAACACTT
* *
40723489 TTTGGTCATTTCCACTCTAAAATTTCCTCAATCTTTTTTGGGTCTACGTAAAATCCCTCCGCAAA
66 TTTGGTCATTTCCACTCTAAAATTTCCTCAATCTTCTTTGGGTCTACGCAAAATCCCTCCGCAAA
*
40723554 ATCCACATAACCCAAGAATGCTACCTCCCTTAACCAAAATTCACACTTGCTGAGCTTCACGAATA
131 ATCCACATAACCCAAGAATGCTACCTCCCTTAACCAAAATTCACACTTCCTGAGCTTCACGAATA
*
40723619 GTTGCTTCTCTCGTAAAATATGTAACACAGTTTGCAGATGAGCATCACCTTAAGTCTTTAAAAGC
196 GTTGCTTCTCTCGTAAAATATGTAACACAGTTTGCAGGTGAGCATCACCTTAAGTCTTTAAAAG-
*
40723684 CTTT-TTGTCTTTCCTCTATCCATGCGAACTCCACATCTTTCTACAGTAGATTTATTATGGGTGT
260 CTTTCTTGACTTTCCTCTATCCATGCGAACTCCACATCTTTCTACAGTAGATTTATTATGGGTGT
40723748 CGCAATGGTGGCGA
325 CGCAATGGTGGCGA
* * *
40723762 ACCCTTCCACAAACTTGCCATAGTATTCTACTAACCTCATAAAGCTTCGCACCTCAATAACACTT
1 ACCCTTCCACAAACTTGCAATAGTATTCTACTAACCTCATAAAGCTTTGCACCTCAGTAACACTT
* ** * *
40723827 TTTGGTCATTTCCACACTAAAATTTAGTCAATCTTCTTTGGGTCTACGCAAACTCCCTTCGCAAA
66 TTTGGTCATTTCCACTCTAAAATTTCCTCAATCTTCTTTGGGTCTACGCAAAATCCCTCCGCAAA
* * * *
40723892 ATCCACATAACCCAAGAATGCTACCTCCCTTAACCAAAATTTACACTTCCTAAGCTTCATGAAAA
131 ATCCACATAACCCAAGAATGCTACCTCCCTTAACCAAAATTCACACTTCCTGAGCTTCACGAATA
* * * * * * *
40723957 GTTACTTCTCTCGCAGAATTTGTAACATAGTTCGCAGGTGAGAATCA
196 GTTGCTTCTCTCGTAAAATATGTAACACAGTTTGCAGGTGAGCATCA
40724004 TGCTCTTCTT
Statistics
Matches: 532, Mismatches: 46, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
337 1 0.00
338 527 0.99
339 4 0.01
ACGTcount: A:0.29, C:0.27, G:0.12, T:0.32
Consensus pattern (338 bp):
ACCCTTCCACAAACTTGCAATAGTATTCTACTAACCTCATAAAGCTTTGCACCTCAGTAACACTT
TTTGGTCATTTCCACTCTAAAATTTCCTCAATCTTCTTTGGGTCTACGCAAAATCCCTCCGCAAA
ATCCACATAACCCAAGAATGCTACCTCCCTTAACCAAAATTCACACTTCCTGAGCTTCACGAATA
GTTGCTTCTCTCGTAAAATATGTAACACAGTTTGCAGGTGAGCATCACCTTAAGTCTTTAAAAGC
TTTCTTGACTTTCCTCTATCCATGCGAACTCCACATCTTTCTACAGTAGATTTATTATGGGTGTC
GCAATGGTGGCGA
Found at i:40726453 original size:23 final size:23
Alignment explanation
Indices: 40726427--40726548 Score: 208
Period size: 23 Copynumber: 5.3 Consensus size: 23
40726417 ATAAGTGCCA
40726427 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
40726450 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
40726473 CACTGAAAAGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
40726496 CACTGATATGTAGCCGAATCTAC
1 CACTGATATGTAGCCGAAGCTAC
40726519 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
40726542 CACTGAT
1 CACTGAT
40726549 CAATAACACT
Statistics
Matches: 93, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 93 1.00
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.20
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:40731423 original size:19 final size:20
Alignment explanation
Indices: 40731386--40731423 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
40731376 TATGTGTTTT
40731386 GTTCAAATGTAACTTTGTTA
1 GTTCAAATGTAACTTTGTTA
*
40731406 GTTCAATTGTAA-TTTGTT
1 GTTCAAATGTAACTTTGTT
40731424 CAGCAAAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.26, C:0.08, G:0.16, T:0.50
Consensus pattern (20 bp):
GTTCAAATGTAACTTTGTTA
Found at i:40735904 original size:19 final size:20
Alignment explanation
Indices: 40735867--40735904 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
40735857 TATGTGTTTT
40735867 GTTCAAATGTAACTTTGTTA
1 GTTCAAATGTAACTTTGTTA
*
40735887 GTTCAATTGTAA-TTTGTT
1 GTTCAAATGTAACTTTGTT
40735905 CAGCAAAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.26, C:0.08, G:0.16, T:0.50
Consensus pattern (20 bp):
GTTCAAATGTAACTTTGTTA
Found at i:40738377 original size:21 final size:22
Alignment explanation
Indices: 40738347--40738390 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
40738337 TAATATGTTT
40738347 TAAATAGATATAACTATTAAAG
1 TAAATAGATATAACTATTAAAG
* *
40738369 TAAA-AGATATAATTATTCAAG
1 TAAATAGATATAACTATTAAAG
40738390 T
1 T
40738391 GACATCTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.52, C:0.05, G:0.09, T:0.34
Consensus pattern (22 bp):
TAAATAGATATAACTATTAAAG
Found at i:40740682 original size:19 final size:20
Alignment explanation
Indices: 40740639--40740683 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
40740629 AAGATAGCTA
40740639 GATGAGTTGAGAGAATGATG
1 GATGAGTTGAGAGAATGATG
*
40740659 AATGAG-TGAGA-AATGATGG
1 GATGAGTTGAGAGAATGAT-G
40740678 GATGAG
1 GATGAG
40740684 GGATGATTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 6 0.27
19 11 0.50
20 5 0.23
ACGTcount: A:0.38, C:0.00, G:0.40, T:0.22
Consensus pattern (20 bp):
GATGAGTTGAGAGAATGATG
Found at i:40741150 original size:14 final size:14
Alignment explanation
Indices: 40741131--40741158 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
40741121 TTAATTTATT
40741131 AATGAATTATTAAA
1 AATGAATTATTAAA
40741145 AATGAATTATTAAA
1 AATGAATTATTAAA
40741159 TATAACTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (14 bp):
AATGAATTATTAAA
Found at i:40745998 original size:17 final size:17
Alignment explanation
Indices: 40745978--40746011 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
40745968 TTGAAAAAAA
40745978 AAATTCGAAAAAAAAGG
1 AAATTCGAAAAAAAAGG
40745995 AAATTCGAAAAAAAAGG
1 AAATTCGAAAAAAAAGG
40746012 GGGTACGAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.65, C:0.06, G:0.18, T:0.12
Consensus pattern (17 bp):
AAATTCGAAAAAAAAGG
Found at i:40746880 original size:6 final size:6
Alignment explanation
Indices: 40746869--40746977 Score: 83
Period size: 6 Copynumber: 17.7 Consensus size: 6
40746859 ACATTGTAAT
* * ** *
40746869 GAAAAA GAAAAA GAAAAA GAAAAC GAAAAT GAAAAA GAAATT GCAAAA
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA
** ** * * *
40746917 GAAAAA GAAATC GAAAAA GTGAGA GAAAAA GAAAAT GAAGAAAA GAAAATT
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA G-A-AAAA GAAAA-A
40746968 GAAAAA GAAA
1 GAAAAA GAAA
40746978 TTGAGATTGA
Statistics
Matches: 77, Mismatches: 23, Indels: 6
0.73 0.22 0.06
Matches are distributed among these distances:
6 66 0.86
7 7 0.09
8 4 0.05
ACGTcount: A:0.71, C:0.03, G:0.19, T:0.07
Consensus pattern (6 bp):
GAAAAA
Found at i:40746986 original size:18 final size:18
Alignment explanation
Indices: 40746965--40746999 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
40746955 AGAAAAGAAA
40746965 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
40746983 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
40747000 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Found at i:40747008 original size:16 final size:18
Alignment explanation
Indices: 40746987--40747025 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
40746977 ATTGAGATTG
40746987 AGAAAAA-A-ATTGAAAA
1 AGAAAAAGATATTGAAAA
*
40747003 AGAAAAAGATGTTGAAAA
1 AGAAAAAGATATTGAAAA
40747021 AGAAA
1 AGAAA
40747026 CGAGAGGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 7 0.35
17 1 0.05
18 12 0.60
ACGTcount: A:0.69, C:0.00, G:0.18, T:0.13
Consensus pattern (18 bp):
AGAAAAAGATATTGAAAA
Found at i:40749059 original size:13 final size:13
Alignment explanation
Indices: 40749041--40749069 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
40749031 TGTGTTTTGC
40749041 TGCTGTTGTTTAA
1 TGCTGTTGTTTAA
40749054 TGCTGTTGTTTAA
1 TGCTGTTGTTTAA
40749067 TGC
1 TGC
40749070 AGAATATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.14, C:0.10, G:0.24, T:0.52
Consensus pattern (13 bp):
TGCTGTTGTTTAA
Found at i:40771210 original size:219 final size:219
Alignment explanation
Indices: 40770831--40771271 Score: 882
Period size: 219 Copynumber: 2.0 Consensus size: 219
40770821 TCGTTTGATC
40770831 GTTTATTGATTGTAGAGATATGCTTGCTTCTGTTTTTTTTTTTCCTTCCATTCATAGATGTACAC
1 GTTTATTGATTGTAGAGATATGCTTGCTTCTGTTTTTTTTTTTCCTTCCATTCATAGATGTACAC
40770896 GATTTGTTCTCAACTTCTTTTAAGTTGATAATACATATAAAATGATAATACACATATGATTACAG
66 GATTTGTTCTCAACTTCTTTTAAGTTGATAATACATATAAAATGATAATACACATATGATTACAG
40770961 GGACATATAATGGAGTACGTAGAGCCTATCTTTTGCATTGCAAATTGTCTCGGAACTCCAGTTTG
131 GGACATATAATGGAGTACGTAGAGCCTATCTTTTGCATTGCAAATTGTCTCGGAACTCCAGTTTG
40771026 TAAATACTTGCAGTATCACAGAAA
196 TAAATACTTGCAGTATCACAGAAA
40771050 GTTTATTGATTGTAGAGATATGCTTGCTTCTGTTTTTTTTTTTCCTTCCATTCATAGATGTACAC
1 GTTTATTGATTGTAGAGATATGCTTGCTTCTGTTTTTTTTTTTCCTTCCATTCATAGATGTACAC
40771115 GATTTGTTCTCAACTTCTTTTAAGTTGATAATACATATAAAATGATAATACACATATGATTACAG
66 GATTTGTTCTCAACTTCTTTTAAGTTGATAATACATATAAAATGATAATACACATATGATTACAG
40771180 GGACATATAATGGAGTACGTAGAGCCTATCTTTTGCATTGCAAATTGTCTCGGAACTCCAGTTTG
131 GGACATATAATGGAGTACGTAGAGCCTATCTTTTGCATTGCAAATTGTCTCGGAACTCCAGTTTG
40771245 TAAATACTTGCAGTATCACAGAAA
196 TAAATACTTGCAGTATCACAGAAA
40771269 GTT
1 GTT
40771272 GAATTATTAT
Statistics
Matches: 222, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
219 222 1.00
ACGTcount: A:0.29, C:0.15, G:0.16, T:0.39
Consensus pattern (219 bp):
GTTTATTGATTGTAGAGATATGCTTGCTTCTGTTTTTTTTTTTCCTTCCATTCATAGATGTACAC
GATTTGTTCTCAACTTCTTTTAAGTTGATAATACATATAAAATGATAATACACATATGATTACAG
GGACATATAATGGAGTACGTAGAGCCTATCTTTTGCATTGCAAATTGTCTCGGAACTCCAGTTTG
TAAATACTTGCAGTATCACAGAAA
Found at i:40775896 original size:11 final size:10
Alignment explanation
Indices: 40775858--40775893 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
40775848 AATTTTAATG
40775858 AAAAATATAA
1 AAAAATATAA
*
40775868 AAATATATAA
1 AAAAATATAA
*
40775878 AAAATTATAA
1 AAAAATATAA
40775888 AAAAAT
1 AAAAAT
40775894 TATTTTTTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (10 bp):
AAAAATATAA
Found at i:40778181 original size:19 final size:19
Alignment explanation
Indices: 40778128--40778181 Score: 60
Period size: 19 Copynumber: 3.0 Consensus size: 19
40778118 GCCATGTGGC
40778128 AAAAATT-ATAAAAA--AT
1 AAAAATTAATAAAAATTAT
* * *
40778144 AAAAATCAATAAGATTTAT
1 AAAAATTAATAAAAATTAT
40778163 AAAAATTAATAAAAATTAT
1 AAAAATTAATAAAAATTAT
40778182 TTAAAATAGA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
16 6 0.21
17 5 0.17
19 18 0.62
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (19 bp):
AAAAATTAATAAAAATTAT
Found at i:40778222 original size:19 final size:19
Alignment explanation
Indices: 40778198--40778261 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 19
40778188 TAGAATAAAT
*
40778198 TATAAATATCGTAAAAAAA
1 TATAAAAATCGTAAAAAAA
* * ***
40778217 TATAAAAATTGCAAAATGT
1 TATAAAAATCGTAAAAAAA
*
40778236 TATAAAAATCATAAAAAAA
1 TATAAAAATCGTAAAAAAA
40778255 TATAAAA
1 TATAAAA
40778262 TGCATTAAAA
Statistics
Matches: 33, Mismatches: 12, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.27
Consensus pattern (19 bp):
TATAAAAATCGTAAAAAAA
Found at i:40778537 original size:11 final size:12
Alignment explanation
Indices: 40778514--40778538 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40778504 CTTTATAAAA
40778514 TTTTCTAATTTT
1 TTTTCTAATTTT
40778526 TTTTCTAATTTT
1 TTTTCTAATTTT
40778538 T
1 T
40778539 AATAGATTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTCTAATTTT
Found at i:40778596 original size:20 final size:19
Alignment explanation
Indices: 40778552--40778596 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
40778542 AGATTAAAAT
*
40778552 ATTTTTATATTTTTATTAA
1 ATTTTAATATTTTTATTAA
* *
40778571 AATTTAATATTTTTTTCTAA
1 ATTTTAATATTTTTAT-TAA
40778591 ATTTTA
1 ATTTTA
40778597 TTGATTTCTA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (19 bp):
ATTTTAATATTTTTATTAA
Found at i:40778935 original size:92 final size:91
Alignment explanation
Indices: 40778761--40778936 Score: 237
Period size: 92 Copynumber: 1.9 Consensus size: 91
40778751 CAATTGAGTG
* * *
40778761 CAAAAAAAAAGTAGGGGCTTAATTGCTCTTTTGAAAAAGTTTGAGGGCCTTTTTGATGCATTTTT
1 CAAAAAAAAAATAGGGGCTTAATTGCTCTTTTGAAAAAGTTTGAGGGCCTTTTTAATACATTTTT
* * * *
40778826 GCAGTTCAAGTACCCAATTGAATTTC
66 GAAGTTAAAATAACCAATTGAATTTC
* * *
40778852 CAAAAAAAAAATAGGGGCTTAATTGTTTCTTTTGAAAATGTTTGAGGGTCTTTTTAATACA-TTT
1 CAAAAAAAAAATAGGGGCTTAATTG-CTCTTTTGAAAAAGTTTGAGGGCCTTTTTAATACATTTT
40778916 TGAAAGTTAAAATAACCAATT
65 TG-AAGTTAAAATAACCAATT
40778937 CAGTGAAAAA
Statistics
Matches: 73, Mismatches: 10, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
91 29 0.40
92 44 0.60
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.36
Consensus pattern (91 bp):
CAAAAAAAAAATAGGGGCTTAATTGCTCTTTTGAAAAAGTTTGAGGGCCTTTTTAATACATTTTT
GAAGTTAAAATAACCAATTGAATTTC
Found at i:40779214 original size:86 final size:86
Alignment explanation
Indices: 40779014--40779217 Score: 202
Period size: 86 Copynumber: 2.3 Consensus size: 86
40779004 CAAACCTTTA
* * *
40779014 AAAAAAAACAATTAAGTCCTTACTATTGTTTTTACTCAATTGGATACTTGACTTTTCAAAATGAA
1 AAAAGAAACAATTAAG-CCCTACT-TT-TTTTTACTCAATTGGATACTTGACTATTCAAAATGAA
40779079 TCAAAAAGACCTTCAAACTTTTTC
63 TCAAAAAGACCTTCAAACTTTTTC
* * * * **
40779103 AGAAGAAACAATTAAGCGCT-TTTTTTTTGTACTCAATTGGGTACTTGAACTATT-AAAATTCAT
1 AAAAGAAACAATTAAGCCCTACTTTTTTT-TACTCAATTGGATACTTG-ACTATTCAAAATGAAT
*
40779166 CAAAAAGGCCCTT-AAAC-TTTTC
64 CAAAAA-GACCTTCAAACTTTTTC
**
40779188 AAAAG-AGTAATTAAGCCCCTACTTTTTTTT
1 AAAAGAAACAATTAAG-CCCTACTTTTTTTT
40779218 GGCACTCAAT
Statistics
Matches: 95, Mismatches: 15, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
84 8 0.08
85 17 0.18
86 43 0.45
87 11 0.12
88 2 0.02
89 14 0.15
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.36
Consensus pattern (86 bp):
AAAAGAAACAATTAAGCCCTACTTTTTTTTACTCAATTGGATACTTGACTATTCAAAATGAATCA
AAAAGACCTTCAAACTTTTTC
Found at i:40779509 original size:30 final size:28
Alignment explanation
Indices: 40779433--40779516 Score: 96
Period size: 29 Copynumber: 2.9 Consensus size: 28
40779423 AGAAAAAGAT
* *
40779433 TATAAAATAGTAAAAAATTATAAAATTT
1 TATAAAATCGTAAAAAATTATAAAATTG
*
40779461 TATAAAAATCATAAAAAATATATAAAATTG
1 TAT-AAAATCGTAAAAAAT-TATAAAATTG
* *
40779491 TATAAAGTCGTAAGAAAATTAGAAAA
1 TATAAAATCGTAA-AAAATTATAAAA
40779517 AAAAATGTAA
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
28 3 0.06
29 27 0.57
30 17 0.36
ACGTcount: A:0.61, C:0.02, G:0.07, T:0.30
Consensus pattern (28 bp):
TATAAAATCGTAAAAAATTATAAAATTG
Found at i:40779784 original size:29 final size:30
Alignment explanation
Indices: 40779743--40779817 Score: 86
Period size: 28 Copynumber: 2.6 Consensus size: 30
40779733 TTTTGATTAA
*
40779743 TTTTAAATTATTTTTTCTATTTTTAGT-AAG
1 TTTTAAATTA-TTTTTATATTTTTAGTAAAG
*
40779773 TTTTAAA-TATTTTTATATTTTTATTAAAG
1 TTTTAAATTATTTTTATATTTTTAGTAAAG
*
40779802 -TTT-AATAATTTTTATA
1 TTTTAAATTATTTTTATA
40779818 ACTTTCATTG
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
27 2 0.05
28 26 0.65
29 5 0.12
30 7 0.17
ACGTcount: A:0.32, C:0.01, G:0.04, T:0.63
Consensus pattern (30 bp):
TTTTAAATTATTTTTATATTTTTAGTAAAG
Found at i:40781665 original size:50 final size:50
Alignment explanation
Indices: 40781609--40781715 Score: 187
Period size: 50 Copynumber: 2.1 Consensus size: 50
40781599 TTGCGTAAAA
* *
40781609 TAAAAATCAAACGACATAATCCATTATAGGATTCATCTCCCTAGGTATTT
1 TAAAAATCAAACGACAAAATCCATCATAGGATTCATCTCCCTAGGTATTT
40781659 TAAAAATCAAACGACAAAATCCATCATAGGATTCATCTCCCTAGGTATTT
1 TAAAAATCAAACGACAAAATCCATCATAGGATTCATCTCCCTAGGTATTT
*
40781709 TGAAAAT
1 TAAAAAT
40781716 TAGTTCATAC
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
50 54 1.00
ACGTcount: A:0.40, C:0.20, G:0.10, T:0.30
Consensus pattern (50 bp):
TAAAAATCAAACGACAAAATCCATCATAGGATTCATCTCCCTAGGTATTT
Found at i:40790378 original size:6 final size:6
Alignment explanation
Indices: 40790355--40790424 Score: 61
Period size: 6 Copynumber: 11.5 Consensus size: 6
40790345 TAAGTCCGAC
* * * * * *
40790355 AAATAA AATAAAA AAATAA CAATAA AAATAT AATTAC AATTAA AAATAA
1 AAATAA AA-ATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA
40790404 AAATAA AAA-ATA AAATAA AAA
1 AAATAA AAATA-A AAATAA AAA
40790425 ATTATAAAAC
Statistics
Matches: 52, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
5 1 0.02
6 45 0.87
7 6 0.12
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.20
Consensus pattern (6 bp):
AAATAA
Found at i:40790383 original size:12 final size:13
Alignment explanation
Indices: 40790355--40790426 Score: 67
Period size: 13 Copynumber: 5.3 Consensus size: 13
40790345 TAAGTCCGAC
40790355 AAATAA-AATAAAA
1 AAATAACAAT-AAA
40790368 AAATAACAATAAA
1 AAATAACAATAAA
*
40790381 AATATAATTACAATTAA
1 AA-AT-A--ACAATAAA
*
40790398 AAATAAAAATAAA
1 AAATAACAATAAA
40790411 AAATAA-AATAAA
1 AAATAACAATAAA
40790423 AAAT
1 AAAT
40790427 TATAAAACTA
Statistics
Matches: 51, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
12 10 0.20
13 23 0.45
14 5 0.10
15 2 0.04
16 2 0.04
17 9 0.18
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (13 bp):
AAATAACAATAAA
Found at i:40809001 original size:18 final size:18
Alignment explanation
Indices: 40808975--40809019 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
40808965 CGTTCGTTTC
40808975 CAAAACATTATTC-ATTT
1 CAAAACATTATTCAATTT
*
40808992 ACAAATCATTATTCAATTT
1 -CAAAACATTATTCAATTT
40809011 CAAAACATT
1 CAAAACATT
40809020 TTCTTATTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 20 0.83
19 4 0.17
ACGTcount: A:0.44, C:0.18, G:0.00, T:0.38
Consensus pattern (18 bp):
CAAAACATTATTCAATTT
Found at i:40822395 original size:20 final size:20
Alignment explanation
Indices: 40822370--40822410 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
40822360 TTCAGAACGT
40822370 ATGCCATATTTAAAATAGTA
1 ATGCCATATTTAAAATAGTA
40822390 ATGCCATATTTAAAATAGTA
1 ATGCCATATTTAAAATAGTA
40822410 A
1 A
40822411 GAAGGAACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.34
Consensus pattern (20 bp):
ATGCCATATTTAAAATAGTA
Found at i:40826077 original size:26 final size:26
Alignment explanation
Indices: 40826040--40826131 Score: 91
Period size: 26 Copynumber: 3.5 Consensus size: 26
40826030 AGCTAATAAC
*
40826040 ATTATAAAATTAAAGGAATCAAATTAT
1 ATTA-AAAATTAAAGAAATCAAATTAT
*
40826067 ATTAAAAATTAAA-ACATAT-AAATTAA
1 ATTAAAAATTAAAGA-A-ATCAAATTAT
* *
40826093 ATCT-AAAATTAAAGAAACCAAATTTT
1 AT-TAAAAATTAAAGAAATCAAATTAT
40826119 ATTAAAAATTAAA
1 ATTAAAAATTAAA
40826132 TTAAGTATAT
Statistics
Matches: 54, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
25 2 0.04
26 44 0.81
27 8 0.15
ACGTcount: A:0.60, C:0.05, G:0.03, T:0.32
Consensus pattern (26 bp):
ATTAAAAATTAAAGAAATCAAATTAT
Found at i:40833197 original size:138 final size:138
Alignment explanation
Indices: 40832948--40833496 Score: 496
Period size: 138 Copynumber: 4.0 Consensus size: 138
40832938 AAACTATCAT
*** * * * * * *
40832948 CAGTAAAAACAAGGTTTGTAGACGAAGAGCCGCAACCTTTAAAATAGTTAGTGAGAGCAAAGCTC
1 CAGTAAAAACAAGGTTCACAGGCGAAGAGCCACAGCCTCTAAAACAGTTAGCGAGAGCAAAGCTC
** * * * * *
40833013 CCAACAATGAAAACAAGGTTCGTAGGCAAAGAGCCGTATCCTCTAAAATAGTTAGCGAGAGAAAA
66 CCAACTGTAAAAACAAGGTTCGCAGGCAAAGAGCCGCAGCCTCTAAAATAGTTAGCGAGAGTAAA
*
40833078 GCTCTCAA
131 GCTCCCAA
* ** * * *
40833086 CAGTAAAAATAAGGTTTGCAGGTGAAGAGTCACAGCCTTTAAAACAGTTAGCGAGAGCAAAGCTC
1 CAGTAAAAACAAGGTTCACAGGCGAAGAGCCACAGCCTCTAAAACAGTTAGCGAGAGCAAAGCTC
* * * * *
40833151 CCAACTGTAAAAATAAGGCTCGCAGGCAAAGAGCCGCAGTCACTAAAATAGTTAAC--GAGTAAA
66 CCAACTGTAAAAACAAGGTTCGCAGGCAAAGAGCCGCAGCCTCTAAAATAGTTAGCGAGAGTAAA
*
40833214 GCTCCCAG
131 GCTCCCAA
* * * * ** * *
40833222 CTGTGAAAACAATGTTCACAGGTGAAGAGCCGTAGCCTCTAAAACAGTTAGCTAGAGCAAACCTC
1 CAGTAAAAACAAGGTTCACAGGCGAAGAGCCACAGCCTCTAAAACAGTTAGCGAGAGCAAAGCTC
* ** * * * * * * *
40833287 CTAGTTGCAAAAACAAGGTTTGTAGGCTATA-AGCTGCAGCCTTTAAAACAGTTAGCGAGAGTAA
66 CCAACTGTAAAAACAAGGTTCGCAGGC-AAAGAGCCGCAGCCTCTAAAATAGTTAGCGAGAGTAA
40833351 AGCTCCCAA
130 AGCTCCCAA
* * * * * *
40833360 CTA-TGAAAACAAGGTTCATAGGCGAAAAACCACAGCCTCTAATACAATTAGCGAGAGCAAAGCT
1 C-AGTAAAAACAAGGTTCACAGGCGAAGAGCCACAGCCTCTAAAACAGTTAGCGAGAGCAAAGCT
* * ** * *
40833424 CCCAGCTGTAAAAATAAGGTTCGCAGG-AGAAGATTCGCAGCCTCTAAAATAGATAGCAAGAGTA
65 CCCAACTGTAAAAACAAGGTTCGCAGGCA-AAGAGCCGCAGCCTCTAAAATAGTTAGCGAGAGTA
*
40833488 AAGTTCCCA
129 AAGCTCCCA
40833497 GTTGTAAAAC
Statistics
Matches: 327, Mismatches: 78, Indels: 12
0.78 0.19 0.03
Matches are distributed among these distances:
136 104 0.32
137 3 0.01
138 220 0.67
ACGTcount: A:0.39, C:0.20, G:0.22, T:0.19
Consensus pattern (138 bp):
CAGTAAAAACAAGGTTCACAGGCGAAGAGCCACAGCCTCTAAAACAGTTAGCGAGAGCAAAGCTC
CCAACTGTAAAAACAAGGTTCGCAGGCAAAGAGCCGCAGCCTCTAAAATAGTTAGCGAGAGTAAA
GCTCCCAA
Found at i:40833497 original size:69 final size:69
Alignment explanation
Indices: 40832950--40833505 Score: 413
Period size: 69 Copynumber: 8.1 Consensus size: 69
40832940 ACTATCATCA
* * * * * *
40832950 GTAAAAACAAGGTTTGTA-GACGAAGAGCCGCAACCTTTAAAATAGTTAGTGAGAGCAAAGCTCC
1 GTAAAAACAAGGTTCGCAGGA-GAAGAGCCGCAGCCTCTAAAACAGTTAGCGAGAGCAAAGCTCC
* *
40833014 CAACA
65 CAGCT
* * * * * * * *
40833019 ATGAAAACAAGGTTCGTAGGCA-AAGAGCCGTATCCTCTAAAATAGTTAGCGAGAGAAAAGCTCT
1 GTAAAAACAAGGTTCGCAGG-AGAAGAGCCGCAGCCTCTAAAACAGTTAGCGAGAGCAAAGCTCC
* *
40833083 CAACA
65 CAGCT
* * * * * *
40833088 GTAAAAATAAGGTTTGCAGGTGAAGAGTCACAGCCTTTAAAACAGTTAGCGAGAGCAAAGCTCCC
1 GTAAAAACAAGGTTCGCAGGAGAAGAGCCGCAGCCTCTAAAACAGTTAGCGAGAGCAAAGCTCCC
*
40833153 AACT
66 AGCT
* * * * * * *
40833157 GTAAAAATAAGGCTCGCAGGCA-AAGAGCCGCAGTCACTAAAATAGTTAAC--GAGTAAAGCTCC
1 GTAAAAACAAGGTTCGCAGG-AGAAGAGCCGCAGCCTCTAAAACAGTTAGCGAGAGCAAAGCTCC
40833219 CAGCT
65 CAGCT
* * * * * * * *
40833224 GTGAAAACAATGTTCACAGGTGAAGAGCCGTAGCCTCTAAAACAGTTAGCTAGAGCAAACCTCCT
1 GTAAAAACAAGGTTCGCAGGAGAAGAGCCGCAGCCTCTAAAACAGTTAGCGAGAGCAAAGCTCCC
*
40833289 AGTT
66 AGCT
* * * ** * * *
40833293 GCAAAAACAAGGTTTGTAGGCTATA-AGCTGCAGCCTTTAAAACAGTTAGCGAGAGTAAAGCTCC
1 GTAAAAACAAGGTTCGCAGGAGA-AGAGCCGCAGCCTCTAAAACAGTTAGCGAGAGCAAAGCTCC
*
40833357 CAACT
65 CAGCT
* * ** * * * * * *
40833362 ATGAAAACAAGGTTCATAGGCGAAAAACCACAGCCTCTAATACAATTAGCGAGAGCAAAGCTCCC
1 GTAAAAACAAGGTTCGCAGGAGAAGAGCCGCAGCCTCTAAAACAGTTAGCGAGAGCAAAGCTCCC
40833427 AGCT
66 AGCT
* ** * * * * *
40833431 GTAAAAATAAGGTTCGCAGGAGAAGATTCGCAGCCTCTAAAATAGATAGCAAGAGTAAAGTTCCC
1 GTAAAAACAAGGTTCGCAGGAGAAGAGCCGCAGCCTCTAAAACAGTTAGCGAGAGCAAAGCTCCC
*
40833496 AGTT
66 AGCT
40833500 GTAAAA
1 GTAAAA
40833506 CCAAAGCTTG
Statistics
Matches: 378, Mismatches: 100, Indels: 18
0.76 0.20 0.04
Matches are distributed among these distances:
67 53 0.14
68 1 0.00
69 321 0.85
70 2 0.01
71 1 0.00
ACGTcount: A:0.39, C:0.20, G:0.22, T:0.19
Consensus pattern (69 bp):
GTAAAAACAAGGTTCGCAGGAGAAGAGCCGCAGCCTCTAAAACAGTTAGCGAGAGCAAAGCTCCC
AGCT
Found at i:40833728 original size:54 final size:54
Alignment explanation
Indices: 40833562--40833731 Score: 173
Period size: 54 Copynumber: 3.2 Consensus size: 54
40833552 AGAGAAAACC
* * *
40833562 TCTTAAGTATGAAATAGCTCGCGGATTTGTATTCCCAGTTATGAATTTTAAAAT
1 TCTTAAGTATAAAATAGCTCACGGATTTGTATTCCCAGCTATGAATTTTAAAAT
* * * * * *** *
40833616 T-TTAAGTATAGAATAGCTCACAGG-TTTATACTCCCAACTGTGAATAAAAAAAC
1 TCTTAAGTATAAAATAGCTCAC-GGATTTGTATTCCCAGCTATGAATTTTAAAAT
* * * *
40833669 CCTTAAGTACAAAATAGCTTACGGATTCGTATTCCCAGCTATGAATTTTAAAAT
1 TCTTAAGTATAAAATAGCTCACGGATTTGTATTCCCAGCTATGAATTTTAAAAT
40833723 TCTTAAGTA
1 TCTTAAGTA
40833732 GAGAACAGTT
Statistics
Matches: 87, Mismatches: 26, Indels: 6
0.73 0.22 0.05
Matches are distributed among these distances:
53 39 0.45
54 48 0.55
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (54 bp):
TCTTAAGTATAAAATAGCTCACGGATTTGTATTCCCAGCTATGAATTTTAAAAT
Done.