Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397268.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_81.0, whole genome shotgun sequence
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: 6219335
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 77647 characters in sequence are not A, C, G, or T
File 8 of 13
Found at i:4012884 original size:2 final size:2
Alignment explanation
Indices: 4012877--4012902 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4012867 CATTCATGAA
4012877 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
4012903 TCATAAATAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4013079 original size:15 final size:15
Alignment explanation
Indices: 4013059--4013087 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
4013049 GAAGCTTTCT
4013059 GGAAGTTGATGAAAG
1 GGAAGTTGATGAAAG
4013074 GGAAGTTGATGAAA
1 GGAAGTTGATGAAA
4013088 AGTTGATCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.38, T:0.21
Consensus pattern (15 bp):
GGAAGTTGATGAAAG
Found at i:4015586 original size:21 final size:21
Alignment explanation
Indices: 4015562--4015603 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
4015552 ACTTAGAGAA
4015562 AGTTTATGCAAATGTGAGCTT
1 AGTTTATGCAAATGTGAGCTT
4015583 AGTTTATGCAAATGTGAGCTT
1 AGTTTATGCAAATGTGAGCTT
4015604 TTGAAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.10, G:0.24, T:0.38
Consensus pattern (21 bp):
AGTTTATGCAAATGTGAGCTT
Found at i:4023929 original size:17 final size:19
Alignment explanation
Indices: 4023893--4023930 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
4023883 ATATTGTAAT
*
4023893 TATTTTTAACAGATAAAAA
1 TATTTTTAACAGACAAAAA
4023912 TATTTTTAA-A-ACAAAAA
1 TATTTTTAACAGACAAAAA
4023929 TA
1 TA
4023931 AAAATTTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 8 0.44
18 1 0.06
19 9 0.50
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.37
Consensus pattern (19 bp):
TATTTTTAACAGACAAAAA
Found at i:4024324 original size:30 final size:30
Alignment explanation
Indices: 4024288--4024349 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
4024278 AAATAAATTT
4024288 TATTTTT-TATTACATCTA-ATTAAGTTTTTA
1 TATTTTTATATTA-ATCTATATTAA-TTTTTA
* *
4024318 TATTTTTATTTTAATTTATATTAATTTTTA
1 TATTTTTATATTAATCTATATTAATTTTTA
4024348 TA
1 TA
4024350 ATTAATATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 19 0.68
31 9 0.32
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.65
Consensus pattern (30 bp):
TATTTTTATATTAATCTATATTAATTTTTA
Found at i:4024359 original size:31 final size:28
Alignment explanation
Indices: 4024306--4024379 Score: 73
Period size: 30 Copynumber: 2.6 Consensus size: 28
4024296 ATTACATCTA
**
4024306 ATTAAGTTTTTATATTTTTATTTTAATTTAT
1 ATTAA-TTTTTATATTAATA-TTT-ATTTAT
4024337 ATTAATTTTTATAATTAATATTTATTTAT
1 ATTAATTTTTAT-ATTAATATTTATTTAT
4024366 -TT-ATTTTTA-ATTAA
1 ATTAATTTTTATATTAA
4024380 AAAATCACTT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
25 5 0.12
27 7 0.17
28 2 0.05
29 6 0.15
30 10 0.25
31 10 0.25
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.65
Consensus pattern (28 bp):
ATTAATTTTTATATTAATATTTATTTAT
Found at i:4024367 original size:23 final size:22
Alignment explanation
Indices: 4024318--4024367 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 22
4024308 TAAGTTTTTA
*
4024318 TATTTTTATTTTAATTTATATT
1 TATTTTTATATTAATTTATATT
*
4024340 AATTTTTATAATTAATATT-TATT
1 TATTTTTAT-ATTAAT-TTATATT
4024363 TATTT
1 TATTT
4024368 ATTTTTAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
22 8 0.35
23 13 0.57
24 2 0.09
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (22 bp):
TATTTTTATATTAATTTATATT
Found at i:4024376 original size:25 final size:25
Alignment explanation
Indices: 4024318--4024380 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 25
4024308 TAAGTTTTTA
* *
4024318 TATTTTTATTTTAATTTATATTAAT
1 TATTTTTAATTAAATTTATATTAAT
* *
4024343 T-TTTATAATTAATATTTAT-TTATT
1 TATTTTTAATTAA-ATTTATATTAAT
4024367 TATTTTTAATTAAA
1 TATTTTTAATTAAA
4024381 AAATCACTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
24 14 0.45
25 17 0.55
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (25 bp):
TATTTTTAATTAAATTTATATTAAT
Found at i:4024442 original size:33 final size:33
Alignment explanation
Indices: 4024405--4024469 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 33
4024395 TTTATGTCAC
* *
4024405 ATAATAAAATGACATATTAATATATTATGATAG
1 ATAATAAAATAACATACTAATATATTATGATAG
* * *
4024438 ATAATGATATAACATACTAATGTATTATGATA
1 ATAATAAAATAACATACTAATATATTATGATA
4024470 ATATTAATAC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.49, C:0.05, G:0.09, T:0.37
Consensus pattern (33 bp):
ATAATAAAATAACATACTAATATATTATGATAG
Found at i:4027312 original size:18 final size:18
Alignment explanation
Indices: 4027289--4027326 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
4027279 TTAAATCGAT
4027289 TCAATTTAATCGAA-TTAA
1 TCAATTTAATC-AACTTAA
4027307 TCAATTTAATCAACTTAA
1 TCAATTTAATCAACTTAA
4027325 TC
1 TC
4027327 GAATCAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 2 0.11
18 17 0.89
ACGTcount: A:0.42, C:0.16, G:0.03, T:0.39
Consensus pattern (18 bp):
TCAATTTAATCAACTTAA
Found at i:4027342 original size:9 final size:9
Alignment explanation
Indices: 4027289--4027326 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
4027279 TTAAATCGAT
4027289 TCAATTTAA
1 TCAATTTAA
4027298 TCGAA-TTAA
1 TC-AATTTAA
4027307 TCAATTTAA
1 TCAATTTAA
*
4027316 TCAACTTAA
1 TCAATTTAA
4027325 TC
1 TC
4027327 GAATCAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
8 2 0.08
9 22 0.85
10 2 0.08
ACGTcount: A:0.42, C:0.16, G:0.03, T:0.39
Consensus pattern (9 bp):
TCAATTTAA
Found at i:4028669 original size:8 final size:8
Alignment explanation
Indices: 4028656--4028764 Score: 50
Period size: 8 Copynumber: 14.1 Consensus size: 8
4028646 AGAGCAGCTA
4028656 AGAGAAAG
1 AGAGAAAG
4028664 AGAGAAAG
1 AGAGAAAG
*
4028672 -GAGGAAG
1 AGAGAAAG
* ***
4028679 AGCGGCTG
1 AGAGAAAG
4028687 AGAGAAAG
1 AGAGAAAG
*
4028695 AGGGAAAG
1 AGAGAAAG
*
4028703 -GAGGAAG
1 AGAGAAAG
* * **
4028710 TGCGATTG
1 AGAGAAAG
4028718 AGAGAAAG
1 AGAGAAAG
4028726 AG-GCAAAG
1 AGAG-AAAG
4028734 -GAGAAAG
1 AGAGAAAG
4028741 A-AGGAAAG
1 AGA-GAAAG
*
4028749 -GAGGAAG
1 AGAGAAAG
4028756 AGAGAAAG
1 AGAGAAAG
4028764 A
1 A
4028765 AAAAAATGTT
Statistics
Matches: 72, Mismatches: 21, Indels: 16
0.66 0.19 0.15
Matches are distributed among these distances:
7 22 0.31
8 50 0.69
ACGTcount: A:0.50, C:0.04, G:0.43, T:0.04
Consensus pattern (8 bp):
AGAGAAAG
Found at i:4028720 original size:31 final size:31
Alignment explanation
Indices: 4028642--4028741 Score: 121
Period size: 31 Copynumber: 3.2 Consensus size: 31
4028632 AGTGGGATGA
* *
4028642 AGGAAGAGC-AGCTAAGAGAAAGAGAGAAAGG
1 AGGAAGAGCGA-CTGAGAGAAAGAGGGAAAGG
*
4028673 AGGAAGAGCGGCTGAGAGAAAGAGGGAAAGG
1 AGGAAGAGCGACTGAGAGAAAGAGGGAAAGG
* * *
4028704 AGGAAGTGCGATTGAGAGAAAGAGGCAAAGG
1 AGGAAGAGCGACTGAGAGAAAGAGGGAAAGG
*
4028735 AGAAAGA
1 AGGAAGA
4028742 AGGAAAGGAG
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
31 59 1.00
ACGTcount: A:0.47, C:0.06, G:0.42, T:0.05
Consensus pattern (31 bp):
AGGAAGAGCGACTGAGAGAAAGAGGGAAAGG
Found at i:4028739 original size:15 final size:14
Alignment explanation
Indices: 4028719--4028763 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 14
4028709 GTGCGATTGA
4028719 GAGAAAGAGGCAAAG
1 GAGAAAGAGG-AAAG
4028734 GAGAAAGAAGGAAAG
1 GAGAAAG-AGGAAAG
*
4028749 GAGGAAGAGAGAAAG
1 GAGAAAGAG-GAAAG
4028764 AAAAAAATGT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
14 2 0.07
15 22 0.81
16 3 0.11
ACGTcount: A:0.56, C:0.02, G:0.42, T:0.00
Consensus pattern (14 bp):
GAGAAAGAGGAAAG
Found at i:4031415 original size:36 final size:36
Alignment explanation
Indices: 4031340--4031427 Score: 88
Period size: 36 Copynumber: 2.4 Consensus size: 36
4031330 TGACAACTTA
* * * *
4031340 CCTTCTCTCTCTCATTCTTCCTTGGTCGACGACTCT
1 CCTTTTCTCTCTCTTTCTTCCTTGGCCGAAGACTCT
* *
4031376 CCTTTTCTCTCTCTTTTTTCCTTGGCCGAA-AGCTTT
1 CCTTTTCTCTCTCTTTCTTCCTTGGCCGAAGA-CTCT
4031412 CCTTCTTTCTCTCTCT
1 CC-T-TTTCTCTCTCT
4031428 CTCTCTCTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
35 1 0.02
36 30 0.70
37 1 0.02
38 11 0.26
ACGTcount: A:0.07, C:0.36, G:0.09, T:0.48
Consensus pattern (36 bp):
CCTTTTCTCTCTCTTTCTTCCTTGGCCGAAGACTCT
Found at i:4032026 original size:7 final size:7
Alignment explanation
Indices: 4032011--4032049 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
4032001 CGTTTTTTTT
4032011 TTATTTA
1 TTATTTA
*
4032018 TTGTTTA
1 TTATTTA
4032025 TTATTTA
1 TTATTTA
4032032 TTA-TTA
1 TTATTTA
4032038 TTATTTA
1 TTATTTA
4032045 -TATTT
1 TTATTT
4032050 GAAAAACAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
6 11 0.38
7 18 0.62
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.72
Consensus pattern (7 bp):
TTATTTA
Found at i:4033266 original size:72 final size:72
Alignment explanation
Indices: 4033184--4033350 Score: 316
Period size: 72 Copynumber: 2.3 Consensus size: 72
4033174 AGTGGTAGCA
4033184 ATAGATTTATTTAGATTGATAATATATACGTAATATATACGTAGAAAAAGAATATATAGTTAGAT
1 ATAGATTTATTTAGATTGATAATATATACGTAATATATACGTAGAAAAAGAATATATAGTTAGAT
4033249 TTAGAAT
66 TTAGAAT
* *
4033256 ATAGATTTATTTAGATTGATAATATATACGTAATATATATGTAGAAAAGGAATATATAGTTAGAT
1 ATAGATTTATTTAGATTGATAATATATACGTAATATATACGTAGAAAAAGAATATATAGTTAGAT
4033321 TTAGAAT
66 TTAGAAT
4033328 ATAGATTTATTTAGATTGATAAT
1 ATAGATTTATTTAGATTGATAAT
4033351 GTGTACATAG
Statistics
Matches: 93, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
72 93 1.00
ACGTcount: A:0.44, C:0.02, G:0.14, T:0.40
Consensus pattern (72 bp):
ATAGATTTATTTAGATTGATAATATATACGTAATATATACGTAGAAAAAGAATATATAGTTAGAT
TTAGAAT
Found at i:4033270 original size:23 final size:23
Alignment explanation
Indices: 4033243--4033344 Score: 64
Period size: 23 Copynumber: 4.3 Consensus size: 23
4033233 GAATATATAG
4033243 TTAGATTTAGAATATAGATTTAT
1 TTAGATTTAGAATATAGATTTAT
* * * * *
4033266 TTAGATTGATAATATATACGTAAT
1 TTAGATTTAGAATATAGA-TTTAT
* * * *
4033290 ATATATGTAGAA-A-AGGAATATATAG
1 TTAGATTTAGAATATA-G-AT-T-TAT
4033315 TTAGATTTAGAATATAGATTTAT
1 TTAGATTTAGAATATAGATTTAT
4033338 TTAGATT
1 TTAGATT
4033345 GATAATGTGT
Statistics
Matches: 54, Mismatches: 18, Indels: 14
0.63 0.21 0.16
Matches are distributed among these distances:
22 1 0.02
23 25 0.46
24 13 0.24
25 12 0.22
26 2 0.04
27 1 0.02
ACGTcount: A:0.42, C:0.01, G:0.15, T:0.42
Consensus pattern (23 bp):
TTAGATTTAGAATATAGATTTAT
Found at i:4033287 original size:61 final size:61
Alignment explanation
Indices: 4033214--4033390 Score: 219
Period size: 72 Copynumber: 2.7 Consensus size: 61
4033204 AATATATACG
4033214 TAATATATACGTAGAAAAAGAATATATAGTTAGATTTAGAATATAGATTTATTTAGATTGA
1 TAATATATACGTAGAAAAAGAATATATAGTTAGATTTAGAATATAGATTTATTTAGATTGA
4033275 TAATATATACGTAATATATATGTAGAAAAGGAATATATAGTTAGATTTAGAATATAGATTTATTT
1 TAATATATACG-------TA-G-A-AAAA-GAATATATAGTTAGATTTAGAATATAGATTTATTT
4033340 AGATTGA
55 AGATTGA
* * * *
4033347 TAATGTGTACATAGAAAAAGAATATATGGTTAGATTTAGAATAT
1 TAATATATACGTAGAAAAAGAATATATAGTTAGATTTAGAATAT
4033391 GGTTAGGAAC
Statistics
Matches: 101, Mismatches: 4, Indels: 22
0.80 0.03 0.17
Matches are distributed among these distances:
61 35 0.35
62 4 0.04
63 1 0.01
64 1 0.01
65 2 0.02
68 2 0.02
69 1 0.01
70 1 0.01
71 4 0.04
72 50 0.50
ACGTcount: A:0.45, C:0.02, G:0.16, T:0.37
Consensus pattern (61 bp):
TAATATATACGTAGAAAAAGAATATATAGTTAGATTTAGAATATAGATTTATTTAGATTGA
Found at i:4036297 original size:18 final size:18
Alignment explanation
Indices: 4036270--4036305 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
4036260 TCCTTTTTAC
* *
4036270 CTTATTTTATTTTCTTTT
1 CTTATCTTATTTTATTTT
4036288 CTTATCTTATTTTATTTT
1 CTTATCTTATTTTATTTT
4036306 TAGTTAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.14, C:0.11, G:0.00, T:0.75
Consensus pattern (18 bp):
CTTATCTTATTTTATTTT
Found at i:4036453 original size:18 final size:17
Alignment explanation
Indices: 4036425--4036462 Score: 67
Period size: 18 Copynumber: 2.2 Consensus size: 17
4036415 TAAAACTAAT
4036425 AAAATAAGATTAAAATA
1 AAAATAAGATTAAAATA
4036442 AAAATCAAGATTAAAATA
1 AAAAT-AAGATTAAAATA
4036460 AAA
1 AAA
4036463 TGAACTGAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.71, C:0.03, G:0.05, T:0.21
Consensus pattern (17 bp):
AAAATAAGATTAAAATA
Found at i:4037786 original size:19 final size:19
Alignment explanation
Indices: 4037764--4037847 Score: 53
Period size: 19 Copynumber: 4.2 Consensus size: 19
4037754 TAGAAAAGGG
4037764 ATATATAGTTAGATTTAGA
1 ATATATAGTTAGATTTAGA
* * *
4037783 ATATAGATTTATTTAGATTGATA
1 ATAT--A--TAGTTAGATTTAGA
** **
4037806 ATATATACATAGA-AAAGGA
1 ATATATAGTTAGATTTA-GA
4037825 ATATATAGTTAGATTTAGA
1 ATATATAGTTAGATTTAGA
4037844 ATAT
1 ATAT
4037848 GGTTTGGAAC
Statistics
Matches: 47, Mismatches: 12, Indels: 12
0.66 0.17 0.17
Matches are distributed among these distances:
18 1 0.02
19 28 0.60
20 1 0.02
21 2 0.04
23 15 0.32
ACGTcount: A:0.45, C:0.01, G:0.14, T:0.39
Consensus pattern (19 bp):
ATATATAGTTAGATTTAGA
Found at i:4037792 original size:61 final size:61
Alignment explanation
Indices: 4037726--4037847 Score: 235
Period size: 61 Copynumber: 2.0 Consensus size: 61
4037716 TGGTAGAAAA
*
4037726 AGATTTATTTAGATTGATAATATATACATAGAAAAGGGATATATAGTTAGATTTAGAATAT
1 AGATTTATTTAGATTGATAATATATACATAGAAAAGGAATATATAGTTAGATTTAGAATAT
4037787 AGATTTATTTAGATTGATAATATATACATAGAAAAGGAATATATAGTTAGATTTAGAATAT
1 AGATTTATTTAGATTGATAATATATACATAGAAAAGGAATATATAGTTAGATTTAGAATAT
4037848 GGTTTGGAAC
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 60 1.00
ACGTcount: A:0.45, C:0.02, G:0.16, T:0.38
Consensus pattern (61 bp):
AGATTTATTTAGATTGATAATATATACATAGAAAAGGAATATATAGTTAGATTTAGAATAT
Found at i:4039310 original size:21 final size:21
Alignment explanation
Indices: 4039278--4039319 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 21
4039268 GGACAAACTG
4039278 AATAAATGAT-AA-TTAAGAA
1 AATAAATGATAAATTTAAGAA
4039297 AATATAATGAATAAATTTAAGAA
1 AATA-AATG-ATAAATTTAAGAA
4039320 TTAAGGCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
19 4 0.21
20 4 0.21
21 2 0.11
22 2 0.11
23 7 0.37
ACGTcount: A:0.62, C:0.00, G:0.10, T:0.29
Consensus pattern (21 bp):
AATAAATGATAAATTTAAGAA
Found at i:4048429 original size:12 final size:12
Alignment explanation
Indices: 4048398--4048440 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
4048388 TTTTTAATTT
*
4048398 TTATTATTATAA
1 TTATTTTTATAA
* *
4048410 GTACTTTTATAA
1 TTATTTTTATAA
4048422 TTATTTTT-TAA
1 TTATTTTTATAA
4048433 TTATTTTT
1 TTATTTTT
4048441 TTAAAAAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
11 11 0.42
12 15 0.58
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (12 bp):
TTATTTTTATAA
Found at i:4053973 original size:22 final size:22
Alignment explanation
Indices: 4053931--4053974 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
4053921 NNNNNNNNNN
4053931 ATATTATATAAAAATATTTTTT
1 ATATTATATAAAAATATTTTTT
*
4053953 ATATTTTA-AAAAAT-TTATTTT
1 ATATTATATAAAAATATT-TTTT
4053974 A
1 A
4053975 AATAAATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 2 0.10
21 11 0.55
22 7 0.35
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
ATATTATATAAAAATATTTTTT
Found at i:4056629 original size:39 final size:39
Alignment explanation
Indices: 4056575--4056652 Score: 120
Period size: 39 Copynumber: 2.0 Consensus size: 39
4056565 TGTTCTCTTC
* *
4056575 GTAATTAGTTTGTCCTTTTTTTCTATCAAAAGAATCTAT
1 GTAATTAGTTTGTCCTTTCTTTCAATCAAAAGAATCTAT
**
4056614 GTAATTAGTTTGTCCTTTCTTTCAATTGAAAGAATCTAT
1 GTAATTAGTTTGTCCTTTCTTTCAATCAAAAGAATCTAT
4056653 TTTTCGTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.28, C:0.13, G:0.12, T:0.47
Consensus pattern (39 bp):
GTAATTAGTTTGTCCTTTCTTTCAATCAAAAGAATCTAT
Found at i:4069588 original size:21 final size:21
Alignment explanation
Indices: 4069564--4069635 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 21
4069554 TTAAGTATTA
4069564 CATGACTAACTTTGGGCATTG
1 CATGACTAACTTTGGGCATTG
* * *
4069585 CATGACTAATTTTTAGGTATTG
1 CATGACTAA-CTTTGGGCATTG
** * *
4069607 TGTAACTGACTTTGGGCATTG
1 CATGACTAACTTTGGGCATTG
4069628 CATGACTA
1 CATGACTA
4069636 GTTGGTACGC
Statistics
Matches: 36, Mismatches: 14, Indels: 2
0.69 0.27 0.04
Matches are distributed among these distances:
21 22 0.61
22 14 0.39
ACGTcount: A:0.25, C:0.15, G:0.22, T:0.38
Consensus pattern (21 bp):
CATGACTAACTTTGGGCATTG
Found at i:4069598 original size:43 final size:43
Alignment explanation
Indices: 4069546--4069635 Score: 117
Period size: 43 Copynumber: 2.1 Consensus size: 43
4069536 ATATTGCGTA
* *
4069546 ACTAGTTTTTAAGTATTACATGACTAACTTTGGGCATTGCATG
1 ACTAATTTTTAAGTATTACATAACTAACTTTGGGCATTGCATG
* *** *
4069589 ACTAATTTTTAGGTATTGTGTAACTGACTTTGGGCATTGCATG
1 ACTAATTTTTAAGTATTACATAACTAACTTTGGGCATTGCATG
4069632 ACTA
1 ACTA
4069636 GTTGGTACGC
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.40
Consensus pattern (43 bp):
ACTAATTTTTAAGTATTACATAACTAACTTTGGGCATTGCATG
Found at i:4069647 original size:22 final size:23
Alignment explanation
Indices: 4069622--4069695 Score: 87
Period size: 23 Copynumber: 3.3 Consensus size: 23
4069612 CTGACTTTGG
* *
4069622 GCATTGCATGACTAGTTGGT-AC
1 GCATTGCGTGACTAGTTAGTAAC
* *
4069644 GCATTGCGTGACTTGTTAGTAAG
1 GCATTGCGTGACTAGTTAGTAAC
* *
4069667 GCATTACGTGACTAGTTAGTAAG
1 GCATTGCGTGACTAGTTAGTAAC
4069690 GCATTG
1 GCATTG
4069696 TGTGCCTTAG
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
22 17 0.39
23 27 0.61
ACGTcount: A:0.24, C:0.15, G:0.28, T:0.32
Consensus pattern (23 bp):
GCATTGCGTGACTAGTTAGTAAC
Found at i:4069748 original size:22 final size:22
Alignment explanation
Indices: 4069714--4069795 Score: 76
Period size: 22 Copynumber: 3.8 Consensus size: 22
4069704 AGGTATTCAT
* * *
4069714 TAAAAATTGATCATGCAATGCT
1 TAAAAACTAATCATGCAATGCC
* ** *
4069736 TAAAAACCAATCACACAATACC
1 TAAAAACTAATCATGCAATGCC
*
4069758 T-AAAACTAATCATGTAATGCC
1 TAAAAACTAATCATGCAATGCC
*
4069779 TAAAAATTAATCATGCA
1 TAAAAACTAATCATGCA
4069796 GTGATTAAGT
Statistics
Matches: 45, Mismatches: 14, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
21 16 0.36
22 29 0.64
ACGTcount: A:0.48, C:0.20, G:0.07, T:0.26
Consensus pattern (22 bp):
TAAAAACTAATCATGCAATGCC
Found at i:4072330 original size:34 final size:34
Alignment explanation
Indices: 4072287--4072354 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
4072277 TAAATACTTA
*
4072287 ATTTTGGTTAATACTTATTCTCTAAAGAATTATG
1 ATTTTGGTTAATACCTATTCTCTAAAGAATTATG
*
4072321 ATTTTGGTTAATACCTATTCTCTAAATAATTATG
1 ATTTTGGTTAATACCTATTCTCTAAAGAATTATG
4072355 TTACAACATA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.32, C:0.10, G:0.10, T:0.47
Consensus pattern (34 bp):
ATTTTGGTTAATACCTATTCTCTAAAGAATTATG
Found at i:4072423 original size:35 final size:35
Alignment explanation
Indices: 4072376--4072509 Score: 178
Period size: 35 Copynumber: 3.8 Consensus size: 35
4072366 TATTGTACAG
* * * *
4072376 AGAACAACTAGAACAAGTGAAGTGCTACCTCACGC
1 AGAACAATTAGAACAAGTGAAGCGCTACTTCACGT
*
4072411 AGAACAATTAGAACAAGTGAAGCGCTACTTCATGT
1 AGAACAATTAGAACAAGTGAAGCGCTACTTCACGT
*
4072446 AGAACAATTAGAACAAGTGAAGCGCTACTTAACGT
1 AGAACAATTAGAACAAGTGAAGCGCTACTTCACGT
* * * *
4072481 AGAACAATTATAATAAGTAAAGCACTACT
1 AGAACAATTAGAACAAGTGAAGCGCTACT
4072510 CCGTATGAAA
Statistics
Matches: 88, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 88 1.00
ACGTcount: A:0.43, C:0.19, G:0.18, T:0.20
Consensus pattern (35 bp):
AGAACAATTAGAACAAGTGAAGCGCTACTTCACGT
Found at i:4072766 original size:29 final size:29
Alignment explanation
Indices: 4072733--4072795 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 29
4072723 TCTTACCTTG
4072733 TTCTCATATACCTATTCACATACAACTTC
1 TTCTCATATACCTATTCACATACAACTTC
* * ** *
4072762 TTCTCTTGTACCTATTCATGTACAGCTTC
1 TTCTCATATACCTATTCACATACAACTTC
4072791 TTCTC
1 TTCTC
4072796 TTGTACTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.22, C:0.30, G:0.05, T:0.43
Consensus pattern (29 bp):
TTCTCATATACCTATTCACATACAACTTC
Found at i:4072796 original size:29 final size:29
Alignment explanation
Indices: 4072741--4072866 Score: 146
Period size: 29 Copynumber: 4.3 Consensus size: 29
4072731 TGTTCTCATA
** *
4072741 TACCTATTCACATACAACTTCTTCTCTTG
1 TACCTATTCATGTACAGCTTCTTCTCTTG
4072770 TACCTATTCATGTACAGCTTCTTCTCTTG
1 TACCTATTCATGTACAGCTTCTTCTCTTG
* *
4072799 TACTTATTC-TCGTACAGCTTCTTTTCTTG
1 TACCTATTCAT-GTACAGCTTCTTCTCTTG
* * * *
4072828 TACTTGTTCATGTAGAGCTTCTTCTTTTG
1 TACCTATTCATGTACAGCTTCTTCTCTTG
*
4072857 TACCTTTTCA
1 TACCTATTCA
4072867 CGTGTACCTC
Statistics
Matches: 84, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
28 1 0.01
29 82 0.98
30 1 0.01
ACGTcount: A:0.17, C:0.25, G:0.10, T:0.48
Consensus pattern (29 bp):
TACCTATTCATGTACAGCTTCTTCTCTTG
Found at i:4076434 original size:21 final size:20
Alignment explanation
Indices: 4076410--4076460 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 20
4076400 TAATTGGATA
4076410 TATTTTTTACTACT-AAATATT
1 TATTTTTT-CT-CTCAAATATT
*
4076431 TATTTATTTCTCTCATATATT
1 TATTT-TTTCTCTCAAATATT
4076452 TATATTTTT
1 TAT-TTTTT
4076461 TTAAAAGCCT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 2 0.08
21 19 0.73
22 5 0.19
ACGTcount: A:0.27, C:0.10, G:0.00, T:0.63
Consensus pattern (20 bp):
TATTTTTTCTCTCAAATATT
Found at i:4077234 original size:16 final size:16
Alignment explanation
Indices: 4077213--4077243 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4077203 TGTTTTTTCT
4077213 TTTTTCTTTGTTGTTA
1 TTTTTCTTTGTTGTTA
*
4077229 TTTTTCTTTTTTGTT
1 TTTTTCTTTGTTGTT
4077244 TTGTTTTTCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.03, C:0.06, G:0.10, T:0.81
Consensus pattern (16 bp):
TTTTTCTTTGTTGTTA
Found at i:4077250 original size:18 final size:18
Alignment explanation
Indices: 4077202--4077252 Score: 52
Period size: 18 Copynumber: 2.7 Consensus size: 18
4077192 ATCACCTCAC
4077202 TTGTTTTTTCTTT-TTTCT
1 TTGTTTTTT-TTTCTTTCT
4077220 TTGTTGTTATTTTTCTTT-T
1 TTGTT-TT-TTTTTCTTTCT
4077239 TTGTTTTGTTTTTC
1 TTGTTTT-TTTTTC
4077253 AGGTTGTGGT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
18 13 0.45
19 11 0.38
20 5 0.17
ACGTcount: A:0.02, C:0.08, G:0.10, T:0.80
Consensus pattern (18 bp):
TTGTTTTTTTTTCTTTCT
Found at i:4078982 original size:50 final size:49
Alignment explanation
Indices: 4078925--4079066 Score: 155
Period size: 48 Copynumber: 2.9 Consensus size: 49
4078915 TAATGTTTTT
*
4078925 TCTACCTAATCTATTTTTTTAT-AATAAAATATCTTTCCTATTTTTTCTTA
1 TCTACCTAATCTATTTTTTTATGAATAAAATAT-TTT-CTATTTTTTCTAA
* * ** *
4078975 TCTACCTAATCCA-TTTTTAATGGTTAAATTATTTTCTATTTTTTCTAA
1 TCTACCTAATCTATTTTTTTATGAATAAAATATTTTCTATTTTTTCTAA
* * *
4079023 TCTACCTAATTTATTTTTTTATGACT-AAATATTTTTTCATTTTT
1 TCTACCTAATCTATTTTTTTATGAATAAAATATTTTCT-ATTTTT
4079067 CTATATTTTC
Statistics
Matches: 76, Mismatches: 13, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
48 32 0.42
49 25 0.33
50 19 0.25
ACGTcount: A:0.27, C:0.14, G:0.02, T:0.57
Consensus pattern (49 bp):
TCTACCTAATCTATTTTTTTATGAATAAAATATTTTCTATTTTTTCTAA
Found at i:4079069 original size:48 final size:50
Alignment explanation
Indices: 4078925--4079066 Score: 159
Period size: 49 Copynumber: 2.9 Consensus size: 50
4078915 TAATGTTTTT
*
4078925 TCTACCTAATCTATTTTTTTAT-AATAAA-ATATCTTTCCTATTTTTTCTTA
1 TCTACCTAATCTATTTTTTTATGAATAAATATAT-TTT-CTATTTTTTCTAA
* * **
4078975 TCTACCTAATCCA-TTTTTAATGGTTAAAT-TATTTTCTATTTTTTCTAA
1 TCTACCTAATCTATTTTTTTATGAATAAATATATTTTCTATTTTTTCTAA
* * *
4079023 TCTACCTAATTTATTTTTTTATGACTAAATATTTTTTC-ATTTTT
1 TCTACCTAATCTATTTTTTTATGAATAAATATATTTTCTATTTTT
4079067 CTATATTTTC
Statistics
Matches: 77, Mismatches: 11, Indels: 9
0.79 0.11 0.09
Matches are distributed among these distances:
48 23 0.30
49 29 0.38
50 25 0.32
ACGTcount: A:0.27, C:0.14, G:0.02, T:0.57
Consensus pattern (50 bp):
TCTACCTAATCTATTTTTTTATGAATAAATATATTTTCTATTTTTTCTAA
Found at i:4079155 original size:58 final size:58
Alignment explanation
Indices: 4079006--4079163 Score: 223
Period size: 57 Copynumber: 2.7 Consensus size: 58
4078996 GGTTAAATTA
* * *
4079006 TTTTCTATTTTTTCTA--ATCTACCTAATTTATTTTTTTATGACTAAATATTTTTTCAT
1 TTTTCTATATTTTCTATTATCTATCTAATTTA-TTTTTTATAACTAAATATTTTTTCAT
*
4079063 TTTTCTATATTTTCTATTATTTATCTAATTTATTTTTTATAACTAAAT-TTTTTTCAT
1 TTTTCTATATTTTCTATTATCTATCTAATTTATTTTTTATAACTAAATATTTTTTCAT
*
4079120 TTTTCTATATTTTCTATTATCTATCTAAATCTATTTCTTTATAA
1 TTTTCTATATTTTCTATTATCTATCT-AATTTATTT-TTTATAA
4079164 ATATTTTCCA
Statistics
Matches: 91, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
57 49 0.54
58 23 0.25
59 19 0.21
ACGTcount: A:0.26, C:0.11, G:0.01, T:0.62
Consensus pattern (58 bp):
TTTTCTATATTTTCTATTATCTATCTAATTTATTTTTTATAACTAAATATTTTTTCAT
Found at i:4079385 original size:58 final size:58
Alignment explanation
Indices: 4079245--4079385 Score: 210
Period size: 58 Copynumber: 2.4 Consensus size: 58
4079235 ATAGAGATAA
* * * * * *
4079245 TTTATTGCTTGTAATTTTATCATACACCTAGTCTTTTTGTTGGAGACAAAAATTATTG
1 TTTATTGCTTATAATTTTATCAAATACCTAGTCTTCTTGTTAGAGACAAAAATCATTG
* *
4079303 TTTATTGTTTATAATTTTATCAAATACCTCGTCTTCTTGTTAGAGACAAAAATCATTG
1 TTTATTGCTTATAATTTTATCAAATACCTAGTCTTCTTGTTAGAGACAAAAATCATTG
4079361 TTTATTGCTTATAATTTTATCAAAT
1 TTTATTGCTTATAATTTTATCAAAT
4079386 TATTGTTTAT
Statistics
Matches: 74, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
58 74 1.00
ACGTcount: A:0.30, C:0.12, G:0.11, T:0.48
Consensus pattern (58 bp):
TTTATTGCTTATAATTTTATCAAATACCTAGTCTTCTTGTTAGAGACAAAAATCATTG
Found at i:4086887 original size:32 final size:32
Alignment explanation
Indices: 4086843--4086904 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 32
4086833 TAAGACAAAA
*
4086843 TGTGTAAGGTGACTTTTAAATCTCAATGGAAG
1 TGTGTAAGGTGACTTTCAAATCTCAATGGAAG
*
4086875 TGTGTACA-GTGACTTTCAAATTTCAATGGA
1 TGTGTA-AGGTGACTTTCAAATCTCAATGGA
4086905 GAGTTTGATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
32 26 0.96
33 1 0.04
ACGTcount: A:0.31, C:0.11, G:0.23, T:0.35
Consensus pattern (32 bp):
TGTGTAAGGTGACTTTCAAATCTCAATGGAAG
Found at i:4087705 original size:32 final size:34
Alignment explanation
Indices: 4087656--4087727 Score: 103
Period size: 33 Copynumber: 2.2 Consensus size: 34
4087646 TAACAAAATA
* *
4087656 AAATAAAATATATAATAT-AGGAATTAAAAATTT
1 AAATAAAATATAAAATATAAGAAATTAAAAATTT
4087689 AAATAAAA-ATAAAATATAAGAAATTAAAAATTT
1 AAATAAAATATAAAATATAAGAAATTAAAAATTT
*
4087722 ATATAA
1 AAATAA
4087728 TATAAGAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
32 8 0.23
33 27 0.77
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (34 bp):
AAATAAAATATAAAATATAAGAAATTAAAAATTT
Found at i:4087798 original size:34 final size:33
Alignment explanation
Indices: 4087760--4087832 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 33
4087750 TAGAATATAT
* *
4087760 AATATAAAAAATTGTATTAAAGAAATGAAAATAA
1 AATATAAAAAATTATAAT-AAGAAATGAAAATAA
* *
4087794 AATATATAAGATTATAATAAGAAATGAAAATAA
1 AATATAAAAAATTATAATAAGAAATGAAAATAA
*
4087827 ACTATA
1 AATATA
4087833 TGATATTAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
33 20 0.59
34 14 0.41
ACGTcount: A:0.63, C:0.01, G:0.08, T:0.27
Consensus pattern (33 bp):
AATATAAAAAATTATAATAAGAAATGAAAATAA
Found at i:4089737 original size:25 final size:25
Alignment explanation
Indices: 4089704--4089751 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
4089694 ATCTTATCAT
*
4089704 TTTTTGTGTCTTAA-TCGTGTTAATA
1 TTTTCGTGTCTTAACT-GTGTTAATA
4089729 TTTTCGTGTCTTAACTGTGTTAA
1 TTTTCGTGTCTTAACTGTGTTAA
4089752 ACACGGTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 20 0.95
26 1 0.05
ACGTcount: A:0.19, C:0.10, G:0.17, T:0.54
Consensus pattern (25 bp):
TTTTCGTGTCTTAACTGTGTTAATA
Found at i:4093952 original size:39 final size:39
Alignment explanation
Indices: 4093866--4093953 Score: 90
Period size: 40 Copynumber: 2.2 Consensus size: 39
4093856 ATGGGTGCTG
* **
4093866 ACAGGGAAACCAATCTCCAGTTTTTTCCTGTTTGTGCAA
1 ACAGGAAAACCAATCTCCAGTTTTTTCCTAATTGTGCAA
**
4093905 TTAGGGAAAACCAAT-TCCAGTTTTTTCCCTAATTGCT-CAA
1 ACA-GGAAAACCAATCTCCAGTTTTTT-CCTAATTG-TGCAA
4093945 ACAGGAAAA
1 ACAGGAAAA
4093954 AATAGAGTTA
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
39 18 0.46
40 20 0.51
41 1 0.03
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.31
Consensus pattern (39 bp):
ACAGGAAAACCAATCTCCAGTTTTTTCCTAATTGTGCAA
Found at i:4100057 original size:20 final size:20
Alignment explanation
Indices: 4100032--4100072 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
4100022 ATTTTAAACA
4100032 TTTTTAAAAAA-AATAATTTT
1 TTTTTAAAAAATAA-AATTTT
4100052 TTTTTAAAAAATAAAATTTT
1 TTTTTAAAAAATAAAATTTT
4100072 T
1 T
4100073 AAAAAAAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 18 0.90
21 2 0.10
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TTTTTAAAAAATAAAATTTT
Found at i:4100079 original size:19 final size:18
Alignment explanation
Indices: 4100026--4100079 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
4100016 ATATAAATTT
4100026 TAAACATTTTTAAAAAAAA
1 TAAA-ATTTTTAAAAAAAA
** **
4100045 TAATTTTTTTTTAAAAAA
1 TAAAATTTTTAAAAAAAA
4100063 TAAAATTTTTAAAAAAA
1 TAAAATTTTTAAAAAAA
4100080 GAACTTTTGA
Statistics
Matches: 27, Mismatches: 8, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
18 24 0.89
19 3 0.11
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (18 bp):
TAAAATTTTTAAAAAAAA
Found at i:4100087 original size:15 final size:16
Alignment explanation
Indices: 4100053--4100094 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
4100043 AATAATTTTT
*
4100053 TTTTAAAAAATAAAAT
1 TTTTAAAAAATAAAAC
*
4100069 TTTTAAAAAA-AGAAC
1 TTTTAAAAAATAAAAC
4100084 TTTTGAAAAAA
1 TTTT-AAAAAA
4100095 CTCCTGAGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 7 0.30
16 16 0.70
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (16 bp):
TTTTAAAAAATAAAAC
Found at i:4104093 original size:40 final size:41
Alignment explanation
Indices: 4104035--4104118 Score: 143
Period size: 40 Copynumber: 2.1 Consensus size: 41
4104025 ACACATACGA
4104035 TAATTTGATTTAAAACTCCATTTAACGGTCATTTTATTGAC
1 TAATTTGATTTAAAACTCCATTTAACGGTCATTTTATTGAC
* *
4104076 TAATTTGA-TTAAAACTCCGTTTAACGGTCATTTTATTGGC
1 TAATTTGATTTAAAACTCCATTTAACGGTCATTTTATTGAC
4104116 TAA
1 TAA
4104119 CCGCAAAAGC
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
40 33 0.80
41 8 0.20
ACGTcount: A:0.31, C:0.14, G:0.12, T:0.43
Consensus pattern (41 bp):
TAATTTGATTTAAAACTCCATTTAACGGTCATTTTATTGAC
Found at i:4104203 original size:7 final size:7
Alignment explanation
Indices: 4104193--4104231 Score: 78
Period size: 7 Copynumber: 5.6 Consensus size: 7
4104183 TGTGATTTGA
4104193 AACTTGC
1 AACTTGC
4104200 AACTTGC
1 AACTTGC
4104207 AACTTGC
1 AACTTGC
4104214 AACTTGC
1 AACTTGC
4104221 AACTTGC
1 AACTTGC
4104228 AACT
1 AACT
4104232 CATGGTTTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.31, C:0.28, G:0.13, T:0.28
Consensus pattern (7 bp):
AACTTGC
Found at i:4104844 original size:5 final size:5
Alignment explanation
Indices: 4104829--4104871 Score: 50
Period size: 5 Copynumber: 8.2 Consensus size: 5
4104819 CTTCTCCGAA
* *
4104829 TATTGT TATTT TATTT TATTT TGTTT TATTT TACTTT TCTTT T
1 TATT-T TATTT TATTT TATTT TATTT TATTT TA-TTT TATTT T
4104872 TCACTCCAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
5 25 0.76
6 8 0.24
ACGTcount: A:0.14, C:0.05, G:0.05, T:0.77
Consensus pattern (5 bp):
TATTT
Found at i:4120778 original size:12 final size:12
Alignment explanation
Indices: 4120756--4120798 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
4120746 GCTTATGGTA
*
4120756 GTGGAGAAGGTG
1 GTGGAGGAGGTG
*
4120768 GTGGTGGAGGTG
1 GTGGAGGAGGTG
*
4120780 GCGGAGGAGGTG
1 GTGGAGGAGGTG
4120792 GTGGAGG
1 GTGGAGG
4120799 TGGCTCTGGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.16, C:0.02, G:0.65, T:0.16
Consensus pattern (12 bp):
GTGGAGGAGGTG
Found at i:4121015 original size:21 final size:21
Alignment explanation
Indices: 4120991--4121056 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
4120981 GGTCTGGATA
4120991 TGGAAGTGGTGGTGGTAGAGG
1 TGGAAGTGGTGGTGGTAGAGG
* * * *
4121012 TGGAAGTAGTGGGGGTGGAAG
1 TGGAAGTGGTGGTGGTAGAGG
* * *
4121033 TGGAGGAGGTGGTGGCAGAGG
1 TGGAAGTGGTGGTGGTAGAGG
4121054 TGG
1 TGG
4121057 CGGTGGCGGC
Statistics
Matches: 34, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.20, C:0.02, G:0.59, T:0.20
Consensus pattern (21 bp):
TGGAAGTGGTGGTGGTAGAGG
Found at i:4121432 original size:14 final size:14
Alignment explanation
Indices: 4121413--4121441 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
4121403 AAATCATGCG
4121413 TTTTTTTTTT-TAA
1 TTTTTTTTTTATAA
4121426 TTTTTTTTTTATAA
1 TTTTTTTTTTATAA
4121440 TT
1 TT
4121442 GGAGAAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTTTTTTTATAA
Found at i:4149000 original size:22 final size:26
Alignment explanation
Indices: 4148940--4148999 Score: 74
Period size: 24 Copynumber: 2.5 Consensus size: 26
4148930 ATATTTTATA
*
4148940 TTTATTA-TTTTTATCTACTATATTT
1 TTTATTACATTTTATCTACTATATTT
*
4148965 TTTATTTCATTTTAT-TA-TATATTT
1 TTTATTACATTTTATCTACTATATTT
4148989 TTT-TTACATTT
1 TTTATTACATTT
4149000 AAGTATTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
23 7 0.23
24 10 0.32
25 8 0.26
26 6 0.19
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (26 bp):
TTTATTACATTTTATCTACTATATTT
Found at i:4169218 original size:2 final size:2
Alignment explanation
Indices: 4169211--4169256 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
4169201 CTCCCAAGTG
4169211 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
4169253 AT AT
1 AT AT
4169257 TGCCTTGGAC
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
Found at i:4171704 original size:28 final size:29
Alignment explanation
Indices: 4171667--4171723 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
4171657 ACTTTATCAT
*
4171667 ATAAAATATTATATTGAT-AT-TTTTAATA
1 ATAAAATATTAAATT-ATAATGTTTTAATA
*
4171695 ATAAATTATTAAATTATAATGTTTTAATA
1 ATAAAATATTAAATTATAATGTTTTAATA
4171724 GTATTTTAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 2 0.08
28 15 0.60
29 8 0.32
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (29 bp):
ATAAAATATTAAATTATAATGTTTTAATA
Found at i:4171803 original size:16 final size:16
Alignment explanation
Indices: 4171771--4171804 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
4171761 AAATAGAGTA
*
4171771 AAAATAAAAAGAAATT
1 AAAATAAAAACAAATT
*
4171787 AAAATAAAAACATATT
1 AAAATAAAAACAAATT
4171803 AA
1 AA
4171805 TATTTTAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.21
Consensus pattern (16 bp):
AAAATAAAAACAAATT
Found at i:4171817 original size:22 final size:21
Alignment explanation
Indices: 4171792--4171832 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
4171782 AAATTAAAAT
4171792 AAAAACATATTAATATTTTAAC
1 AAAAA-ATATTAATATTTTAAC
* *
4171814 AAAAATTATTAATGTTTTA
1 AAAAAATATTAATATTTTA
4171833 CTATTAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.41
Consensus pattern (21 bp):
AAAAAATATTAATATTTTAAC
Found at i:4171841 original size:141 final size:150
Alignment explanation
Indices: 4171687--4171980 Score: 331
Period size: 141 Copynumber: 2.0 Consensus size: 150
4171677 ATATTGATAT
** * * * *
4171687 TTTTAATAATAAATTATTAAATTAT-AATGTTTTAATAGTATTTTAGT-AAAA-TAATT-AAAAA
1 TTTTAATAATAAATTATT-AATTATCAATAATATAATAATATTTCAGTAAAAAGAAATTGAAAAA
** *
4171748 -AAAGGGAGAATGAAAAT-AGAG-T-AAAAATAAAAAGAAATTAAAATAAAA-A-CATATTAATA
65 GAAA-AAAAAATGAAAATCAGAGATAAAAAATAAAAAGAAATTAAAATAAAATATCATATTAATA
4171807 TTTTAACAA-AAATTATTAATG
129 TTTTAACAATAAATTATTAATG
* *
4171828 TTTTACTATTAAATTATTAATTATCAATAATATAATAATATTTCAGTAAAAAAAGAAATTGAAAA
1 TTTTAATAATAAATTATTAATTATCAATAATATAATAATATTTCAGT--AAAAAGAAATTGAAAA
*
4171893 AGAAAAAAAAATGAAAATGACCATAGATAAAAAATAAAAAGAAATTAAAATAAAATATCATATTA
64 AGAAAAAAAAATGAAAAT---CAGAGATAAAAAATAAAAAGAAATTAAAATAAAATATCATATTA
*
4171958 ATATTTTAACAATGAATTATTAA
126 ATATTTTAACAATAAATTATTAA
4171981 ATTATTAGTA
Statistics
Matches: 124, Mismatches: 13, Indels: 18
0.80 0.08 0.12
Matches are distributed among these distances:
140 6 0.05
141 33 0.27
144 4 0.03
145 4 0.03
146 15 0.12
147 3 0.02
150 3 0.02
151 1 0.01
152 26 0.21
153 1 0.01
154 19 0.15
155 9 0.07
ACGTcount: A:0.57, C:0.03, G:0.07, T:0.33
Consensus pattern (150 bp):
TTTTAATAATAAATTATTAATTATCAATAATATAATAATATTTCAGTAAAAAGAAATTGAAAAAG
AAAAAAAAATGAAAATCAGAGATAAAAAATAAAAAGAAATTAAAATAAAATATCATATTAATATT
TTAACAATAAATTATTAATG
Found at i:4188116 original size:36 final size:35
Alignment explanation
Indices: 4188070--4188144 Score: 114
Period size: 36 Copynumber: 2.1 Consensus size: 35
4188060 TTTGAACTTA
*
4188070 AAATATTAAATATAAAACTATAATGTAAAAAATAT
1 AAATATTAAATATAAAACTATAATGCAAAAAATAT
* *
4188105 AAATAGTTAAATATAAAACTATAATGCATAAAATTT
1 AAATA-TTAAATATAAAACTATAATGCAAAAAATAT
4188141 AAAT
1 AAAT
4188145 TTTGATTCTT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
35 5 0.14
36 31 0.86
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.32
Consensus pattern (35 bp):
AAATATTAAATATAAAACTATAATGCAAAAAATAT
Found at i:4190586 original size:47 final size:47
Alignment explanation
Indices: 4190506--4191125 Score: 504
Period size: 47 Copynumber: 13.3 Consensus size: 47
4190496 ACACGGTAAG
* *
4190506 GTTCAAAGTTTGGTGACATGCCATGGAGGGAATCTGTGACACTCTAGA
1 GTTCAGAGTTT-GTGACACGCCATGGAGGGAATCTGTGACACTCTAGA
* * * *
4190554 GTTTAGAGTTTGTGACACACCATGGAGAGAATCTGTGACACTCCAGA
1 GTTCAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACACTCTAGA
* * * * *
4190601 GTTCATAGTTTGTGACACGGCATAGAGGGAGTCTGTGACACGCTAGA
1 GTTCAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACACTCTAGA
* * **
4190648 GTTCAGAG-TT-TGACACGGCATGGATGGAATCTGTGACACGATAGTA
1 GTTCAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACACTCTAG-A
* *
4190694 -TTCAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACA-TGATAGG
1 GTTCAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACACT-CTAGA
* * * * *
4190740 GTTCAGGGTTTGTGACACGCCATGGAGGGAATCTGTAACACGCCAGT
1 GTTCAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACACTCTAGA
* * * *
4190787 GTTCAGAGTTGGTGACACGACATGGAGGGAATCCGTGACA-TGTCAGA
1 GTTCAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACACTCT-AGA
* * * * * *
4190834 GTTTAGAG-GT-TGACATGGCATGGAGGGAATCTGTGACACGAC-AGG
1 GTTCAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACAC-TCTAGA
* * *
4190879 GTTCATG-GTTTGTGACACGCCATGCAGGGAATCTGCGACA-TGCCA-A
1 GTTCA-GAGTTTGTGACACGCCATGGAGGGAATCTGTGACACT-CTAGA
* ** ** * *
4190925 TGTTCAGAGTTGGTGACAC-AAACT--TCGGAATCTGTGACACGCCAGA
1 -GTTCAGAGTTTGTGACACGCCA-TGGAGGGAATCTGTGACACTCTAGA
* * * *
4190971 GTTCAGAG-TT-TGACACGGCATGGATGAAATCTATGACACTAC-AGTA
1 GTTCAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACACT-CTAG-A
* * *
4191017 -TTCAGAGTTTGTGACACACCATGGAGGGAATCTGTGACACGAC-AGG
1 GTTCAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACAC-TCTAGA
* * * * *
4191063 GTTCAGGGTTTGTGACACACCATGGAGGGAATCTGTGAAACGCTAGT
1 GTTCAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACACTCTAGA
*
4191110 GTTCAGAGTTGGTGAC
1 GTTCAGAGTTTGTGAC
4191126 GCGACAGTGA
Statistics
Matches: 459, Mismatches: 84, Indels: 59
0.76 0.14 0.10
Matches are distributed among these distances:
43 7 0.02
44 2 0.00
45 113 0.25
46 16 0.03
47 312 0.68
48 9 0.02
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.25
Consensus pattern (47 bp):
GTTCAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACACTCTAGA
Found at i:4190682 original size:139 final size:140
Alignment explanation
Indices: 4190518--4191201 Score: 596
Period size: 139 Copynumber: 4.9 Consensus size: 140
4190508 TCAAAGTTTG
* * * * *
4190518 GTGACATGCCATGGAGGGAATCTGTGACACTCTAGAGTTTAGAGTTTGTGACACACCATGGAGAG
1 GTGACACGACATGGAGGGAATCTGTGACACGCTAGAGTTCAGAGTTTGTGACACGCCATGGAGAG
* * * * * *
4190583 AATCTGTGACACTCCAGAGTTCATAGTTTGTGACACGGCATAGAGGGAGTCTGTGACACGCTAGA
66 AATCTGTGACACTACAGAGTTCAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACACGCCAGA
4190648 GTTCAGAGTT
131 GTTCAGAGTT
* * * *
4190658 -TGACACGGCATGGATGGAATCTGTGACACGATAGTA-TTCAGAGTTTGTGACACGCCATGGAGG
1 GTGACACGACATGGAGGGAATCTGTGACACGCTAG-AGTTCAGAGTTTGTGACACGCCATGGAGA
* * * *
4190721 GAATCTGTGACA-TGATAGGGTTCAGGGTTTGTGACACGCCATGGAGGGAATCTGTAACACGCCA
65 GAATCTGTGACACT-ACAGAGTTCAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACACGCCA
*
4190785 GTGTTCAGAGTT
129 GAGTTCAGAGTT
* * * * * *
4190797 GGTGACACGACATGGAGGGAATCCGTGACATG-TCAGAGTTTAGAG-GT-TGACATGGCATGGAG
1 -GTGACACGACATGGAGGGAATCTGTGACACGCT-AGAGTTCAGAGTTTGTGACACGCCATGGAG
* * * * * *
4190859 GGAATCTGTGACACGACAGGGTTCATG-GTTTGTGACACGCCATGCAGGGAATCTGCGACATGCC
64 AGAATCTGTGACACTACAGAGTTCA-GAGTTTGTGACACGCCATGGAGGGAATCTGTGACACGCC
4190923 A-ATGTTCAGAGTT
128 AGA-GTTCAGAGTT
* ** * *
4190936 GGTGACAC-AAACT--TCGGAATCTGTGACACGCCAGAGTTCAGAG-TT-TGACACGGCATGGAT
1 -GTGACACGACA-TGGAGGGAATCTGTGACACGCTAGAGTTCAGAGTTTGTGACACGCCATGGA-
* * *
4190996 GA-AATCTATGACACTACAGTA-TTCAGAGTTTGTGACACACCATGGAGGGAATCTGTGACACGA
63 GAGAATCTGTGACACTACAG-AGTTCAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACACGC
* *
4191059 CAGGGTTCAGGGTTT
127 CAGAGTTCAGAG-TT
* * * * * *
4191074 GTGACAC-ACCATGGAGGGAATCTGTGAAACGCTAGTGTTCAGAGTTGGTGACGCGACA-GTGAA
1 GTGACACGA-CATGGAGGGAATCTGTGACACGCTAGAGTTCAGAGTTTGTGACACGCCATG-GAG
* * * * * * * *
4191137 AGACGTTTATGACACAACAGTGTTCAG-GGTTGTGACACGCCACT-AAGAGAATCTGTGACACGC
64 AGA-ATCTGTGACACTACAGAGTTCAGAGTTTGTGACACGCCA-TGGAGGGAATCTGTGACACGC
4191200 CA
127 CA
4191202 TGTGTGTGTC
Statistics
Matches: 445, Mismatches: 73, Indels: 51
0.78 0.13 0.09
Matches are distributed among these distances:
136 1 0.00
137 105 0.24
138 7 0.02
139 229 0.51
140 8 0.02
141 76 0.17
142 19 0.04
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (140 bp):
GTGACACGACATGGAGGGAATCTGTGACACGCTAGAGTTCAGAGTTTGTGACACGCCATGGAGAG
AATCTGTGACACTACAGAGTTCAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACACGCCAGA
GTTCAGAGTT
Found at i:4190856 original size:186 final size:183
Alignment explanation
Indices: 4190491--4191125 Score: 672
Period size: 186 Copynumber: 3.4 Consensus size: 183
4190481 TGTGACAAGG
** * * *
4190491 CTGTGACACGGTAAGGTTCAAAGTTTGGTGACATGCCATGGAGGGAATCTGTGACACT-CTAGAG
1 CTGTGACACGACAGGGTTCAGAGTTT-GTGACACGCCATGGAGGGAATCTGTGACA-TGCTAGAG
* * * *
4190555 TTTAGAGTTTGTGACACACCATGGAGAGAATCTGTGACACTCCAGAGTTCATAGTTTGTGACACG
64 TTCAGAGTTTGTGACAC-CCATGGAGGGAATCTGTGACACGCCAGAGTTCAGAG-TTGTGACACG
* * * *
4190620 GCATAGAGGGAGTCTGTGACACGCTAGAGTTCAGAGTTTGACACGGCATGGATGGAAT
127 GCATGGAGGGAATCTGTGACATGC-AGAGTTCAGAGTTTGACACGGCATGGAGGGAAT
* ** * *
4190678 CTGTGACACGATAGTATTCAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACATGATAGGGTT
1 CTGTGACACGACAGGGTTCAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACATGCTAGAGTT
* * * *
4190743 CAGGGTTTGTGACACGCCATGGAGGGAATCTGTAACACGCCAGTGTTCAGAGTTGGTGACACGAC
66 CAGAGTTTGTGACAC-CCATGGAGGGAATCTGTGACACGCCAGAGTTCAGAGTT-GTGACACGGC
* * * *
4190808 ATGGAGGGAATCCGTGACATGTCAGAGTTTAGAGGTTGACATGGCATGGAGGGAAT
129 ATGGAGGGAATCTGTGACATG-CAGAGTTCAGAGTTTGACACGGCATGGAGGGAAT
* * *
4190864 CTGTGACACGACAGGGTTCATG-GTTTGTGACACGCCATGCAGGGAATCTGCGACATGCCA-ATG
1 CTGTGACACGACAGGGTTCA-GAGTTTGTGACACGCCATGGAGGGAATCTGTGACATGCTAGA-G
* ** **
4190927 TTCAGAGTTGGTGACACAAACT--TCGGAATCTGTGACACGCCAGAGTTCAGAGTT-TGACACGG
64 TTCAGAGTTTGTGACACCCA-TGGAGGGAATCTGTGACACGCCAGAGTTCAGAGTTGTGACACGG
* * * * **
4190989 CATGGATGAAATCTATGACACTACAGTA-TTCAGAGTTTGTGACACACCATGGAGGGAAT
128 CATGGAGGGAATCTGTGACA-TGCAG-AGTTCAGAG-TT-TGACACGGCATGGAGGGAAT
* * * * *
4191048 CTGTGACACGACAGGGTTCAGGGTTTGTGACACACCATGGAGGGAATCTGTGAAACGCTAGTGTT
1 CTGTGACACGACAGGGTTCAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACATGCTAGAGTT
*
4191113 CAGAGTTGGTGAC
66 CAGAGTTTGTGAC
4191126 GCGACAGTGA
Statistics
Matches: 377, Mismatches: 59, Indels: 27
0.81 0.13 0.06
Matches are distributed among these distances:
182 32 0.08
183 4 0.01
184 113 0.30
185 4 0.01
186 201 0.53
187 23 0.06
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.25
Consensus pattern (183 bp):
CTGTGACACGACAGGGTTCAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACATGCTAGAGTT
CAGAGTTTGTGACACCCATGGAGGGAATCTGTGACACGCCAGAGTTCAGAGTTGTGACACGGCAT
GGAGGGAATCTGTGACATGCAGAGTTCAGAGTTTGACACGGCATGGAGGGAAT
Found at i:4191054 original size:23 final size:23
Alignment explanation
Indices: 4191026--4191100 Score: 75
Period size: 23 Copynumber: 3.2 Consensus size: 23
4191016 ATTCAGAGTT
4191026 TGTGACACACCATGGAGGGAATC
1 TGTGACACACCATGGAGGGAATC
* *
4191049 TGTGACACGA-CAGGGTTCAGGG--TT
1 TGTGACAC-ACCATGG---AGGGAATC
4191073 TGTGACACACCATGGAGGGAATC
1 TGTGACACACCATGGAGGGAATC
4191096 TGTGA
1 TGTGA
4191101 AACGCTAGTG
Statistics
Matches: 41, Mismatches: 4, Indels: 14
0.69 0.07 0.24
Matches are distributed among these distances:
21 4 0.10
23 19 0.46
24 14 0.34
26 4 0.10
ACGTcount: A:0.27, C:0.19, G:0.33, T:0.21
Consensus pattern (23 bp):
TGTGACACACCATGGAGGGAATC
Found at i:4192073 original size:31 final size:31
Alignment explanation
Indices: 4192035--4192244 Score: 289
Period size: 31 Copynumber: 6.8 Consensus size: 31
4192025 NNNNNNNNNN
4192035 TATGCATGGCGTGTCACCACCTTTTACTTGT
1 TATGCATGGCGTGTCACCACCTTTTACTTGT
* *
4192066 TATGCATGGCGTGTCACTACTTTTTACTTGT
1 TATGCATGGCGTGTCACCACCTTTTACTTGT
* *
4192097 TATGCATAGCGTGTAACCACC-TTTATCTTGT
1 TATGCATGGCGTGTCACCACCTTTTA-CTTGT
4192128 TATGCATGGCGTGTCACCACCTTTGT-CTTGT
1 TATGCATGGCGTGTCACCACCTTT-TACTTGT
* *
4192159 TATGCATGACGTGTCACTACCTTTTACTTGT
1 TATGCATGGCGTGTCACCACCTTTTACTTGT
* * **
4192190 TATGCATGACGTGCCATTACCTTTTACTTGT
1 TATGCATGGCGTGTCACCACCTTTTACTTGT
*
4192221 TATGCATGGCGTGCCACCACCTTT
1 TATGCATGGCGTGTCACCACCTTT
4192245 CTTTTGTTTT
Statistics
Matches: 160, Mismatches: 15, Indels: 8
0.87 0.08 0.04
Matches are distributed among these distances:
30 5 0.03
31 152 0.95
32 2 0.01
33 1 0.01
ACGTcount: A:0.18, C:0.24, G:0.19, T:0.40
Consensus pattern (31 bp):
TATGCATGGCGTGTCACCACCTTTTACTTGT
Found at i:4194598 original size:555 final size:558
Alignment explanation
Indices: 4193670--4194773 Score: 1901
Period size: 555 Copynumber: 2.0 Consensus size: 558
4193660 GAAAAACATT
* * *
4193670 TTCTCACTCTAGATTTGATTCTCTCTCTCTTACTTTTTTTGTAGAACAATGTTTTTGTTTGCTGA
1 TTCTCACTCTAGATTTGATTCTCTCTCTCTTACTCTTTTTGTAAAACAATGTTTTTATTTGCTGA
* * *
4193735 AAGGTGTGCTATCCTCTTGAACATGTTGAGCTAGAGTTTTAATCTAGGATTATGATGGATGCTAT
66 AAGGTGTACTATCCTCTTGAACATGTTGAGATAGAGTTTTAATCTAGAATTATGATGGATGCTAT
*
4193800 TGTGTAGTTGGAATACTTGAGATTTTTCCTCTACTTGCGTTTATGAGAATATCAATGTTTATTCA
131 TGTGTAGTTGAAATACTTGAGATTTTTCCTCTACTTGCGTTTATGAGAATATCAATGTTTATTCA
*
4193865 AATTCATGCTTATTGTCTCATTTGTTGCTTGATCACCAGTAAGTTGAATAAGGAGCTTTAGATGA
196 AATTCATGCTTATTGTCTCATTTGTTGCTTGATCACCAGCAAGTTGAATAAGGAGCTTTAGATGA
4193930 GGCCTGAAAAGGAAAATCTAAAAGGACCTAAATTTGAGTAATGTATGTTCATCCCATATTAAGAA
261 GGCCTGAAAAGGAAAATCTAAAAGGACCTAAATTTGAGTAATGTATGTTCATCCCATATTAAGAA
*
4193995 ATTAAGTGGGTGATTAATTAATAGGATAGACATATACCTATTAATCATACATAGTCACTATAGGT
326 ATTAAGTGGGTGATTAATTAATAGGATAGACATATACCTATTAATCATACATAGTCACTATAAGT
* *
4194060 CCTAAACTTATTGAGCTTAG-TTTAATTAATGTTCTATAGACTAAAAAAAGAGGAGTTATAAATA
391 CCTAAACTTATTGAACTTAGCTTTAATTAATGTTCTATAGACTAAAAAAAGAGGAGGTATAAATA
4194124 GAAAGTTTT-TCACTAAAAAAGAGAAAGGATTGAGAGAGACCATTTCGGGCAAAAGGAGGCAAGA
456 GAAAGTTTTGT-ACTAAAAAAGAGAAAGGATTGAGAGAGACCATTTCGGGCAAAAGGAGGCAAGA
4194188 ACAAAAAGGAAAAAAGAAGAGGAATCAAGAGCTAGAAGA
520 ACAAAAAGGAAAAAAGAAGAGGAATCAAGAGCTAGAAGA
4194227 TTCTCACTCTAGATTTGA-T-TCTCTCTCTTACTCTTTTTGTAAAACAATGTTTTTATTTGCTGA
1 TTCTCACTCTAGATTTGATTCTCTCTCTCTTACTCTTTTTGTAAAACAATGTTTTTATTTGCTGA
* * * * *
4194290 AATGTGTATTATCTTTTTGAACATGTTGAGATAGAGTTTTAATCTAGAATTATGGTGGATGCTAT
66 AAGGTGTACTATCCTCTTGAACATGTTGAGATAGAGTTTTAATCTAGAATTATGATGGATGCTAT
*
4194355 TGTGTAGTTGAAATACTTGAGATTTTTCCTCTACTTGCTTTTATGAGAATATCAATGTTTATTCA
131 TGTGTAGTTGAAATACTTGAGATTTTTCCTCTACTTGCGTTTATGAGAATATCAATGTTTATTCA
* * * * *
4194420 AATTCATGCTTGTTGTCTCATTTGTTGCTTGATCACTAGCAAGTTGAGTAAGGAGTTTTAGATTA
196 AATTCATGCTTATTGTCTCATTTGTTGCTTGATCACCAGCAAGTTGAATAAGGAGCTTTAGATGA
* *
4194485 GGCCTGAAAAGGACAATCTAAAAGGACCTAAATTTGAGTAATGTATGTTCATCTCATATTAAGAA
261 GGCCTGAAAAGGAAAATCTAAAAGGACCTAAATTTGAGTAATGTATGTTCATCCCATATTAAGAA
4194550 ATTAAGTGGGTGATTAATTAATAGGATAGACATATACCTATTAATCATACATAGTCACTATAAGT
326 ATTAAGTGGGTGATTAATTAATAGGATAGACATATACCTATTAATCATACATAGTCACTATAAGT
*
4194615 CCTAAACTTATTGAACTTAGCTTTAATTAATGTTCTATAGACTAAAAAAAGAGGGGGTATAAATA
391 CCTAAACTTATTGAACTTAGCTTTAATTAATGTTCTATAGACTAAAAAAAGAGGAGGTATAAATA
* * * *
4194680 GAAAGTTTTGTACTGAAAAAGAGAGAGGATTGGGAGAGACCATTTTGGGCAAAAGGAGGCAAGAA
456 GAAAGTTTTGTACTAAAAAAGAGAAAGGATTGAGAGAGACCATTTCGGGCAAAAGGAGGCAAGAA
*
4194745 CAAAAAGGGAAAAAGAAGAGGAATCAAGA
521 CAAAAAGGAAAAAAGAAGAGGAATCAAGA
4194774 NNNNNNNNNN
Statistics
Matches: 515, Mismatches: 30, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
555 366 0.71
556 130 0.25
557 19 0.04
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.34
Consensus pattern (558 bp):
TTCTCACTCTAGATTTGATTCTCTCTCTCTTACTCTTTTTGTAAAACAATGTTTTTATTTGCTGA
AAGGTGTACTATCCTCTTGAACATGTTGAGATAGAGTTTTAATCTAGAATTATGATGGATGCTAT
TGTGTAGTTGAAATACTTGAGATTTTTCCTCTACTTGCGTTTATGAGAATATCAATGTTTATTCA
AATTCATGCTTATTGTCTCATTTGTTGCTTGATCACCAGCAAGTTGAATAAGGAGCTTTAGATGA
GGCCTGAAAAGGAAAATCTAAAAGGACCTAAATTTGAGTAATGTATGTTCATCCCATATTAAGAA
ATTAAGTGGGTGATTAATTAATAGGATAGACATATACCTATTAATCATACATAGTCACTATAAGT
CCTAAACTTATTGAACTTAGCTTTAATTAATGTTCTATAGACTAAAAAAAGAGGAGGTATAAATA
GAAAGTTTTGTACTAAAAAAGAGAAAGGATTGAGAGAGACCATTTCGGGCAAAAGGAGGCAAGAA
CAAAAAGGAAAAAAGAAGAGGAATCAAGAGCTAGAAGA
Found at i:4198855 original size:70 final size:70
Alignment explanation
Indices: 4198748--4198882 Score: 191
Period size: 71 Copynumber: 1.9 Consensus size: 70
4198738 ATGTAAAAAA
* * *
4198748 AGTGAAACTAAAAGCTTAATAACATTACTTTTTAAGA-TTCACTATATTAAAAAATATTTTACCT
1 AGTGAAACTAAAAGCTTAATAACAGTACTTTTTAAGATTTCACTATATAAAAAAATATGTTACCT
4198812 TGAGG
66 TGAGG
* * * *
4198817 AGTGAAATTAAAAGTTTAAATAGCAGTACTTTTTAAGATTTCTCTATATAAAAAAATATGTTACC
1 AGTGAAACTAAAAGCTT-AATAACAGTACTTTTTAAGATTTCACTATATAAAAAAATATGTTACC
4198882 T
65 T
4198883 AAAGAAATGT
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
69 15 0.26
70 18 0.32
71 24 0.42
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.37
Consensus pattern (70 bp):
AGTGAAACTAAAAGCTTAATAACAGTACTTTTTAAGATTTCACTATATAAAAAAATATGTTACCT
TGAGG
Found at i:4198898 original size:71 final size:69
Alignment explanation
Indices: 4198741--4198900 Score: 167
Period size: 71 Copynumber: 2.3 Consensus size: 69
4198731 TTATTAAATG
* * * * *
4198741 TAAAAAAAGTGAAACTAAAAGCTTAATAACATTACTTTTTAAGATTCACTATATTAAAAAATATT
1 TAAAGAAA-TGAAATTAAAAGCTTAATAACAGTACTTTTTAAGATTCACTATATAAAAAAATATG
4198806 TTACC
65 TTACC
** * * * * *
4198811 TTGAGGAGTGAAATTAAAAGTTTAAATAGCAGTACTTTTTAAGATTTCTCTATATAAAAAAATAT
1 TAAAGAAATGAAATTAAAAGCTT-AATAACAGTACTTTTTAAGA-TTCACTATATAAAAAAATAT
4198876 GTTACC
64 GTTACC
**
4198882 TAAAGAAATGTGATTAAAA
1 TAAAGAAATGAAATTAAAA
4198901 CTCAATTTTG
Statistics
Matches: 70, Mismatches: 18, Indels: 3
0.77 0.20 0.03
Matches are distributed among these distances:
69 13 0.19
70 21 0.30
71 36 0.51
ACGTcount: A:0.46, C:0.09, G:0.11, T:0.34
Consensus pattern (69 bp):
TAAAGAAATGAAATTAAAAGCTTAATAACAGTACTTTTTAAGATTCACTATATAAAAAAATATGT
TACC
Found at i:4208333 original size:15 final size:15
Alignment explanation
Indices: 4208313--4208379 Score: 65
Period size: 15 Copynumber: 4.8 Consensus size: 15
4208303 AAATTATAAA
*
4208313 TAAAATATTAGTATT
1 TAAAATATTAATATT
4208328 TAAAATATTAATGA-T
1 TAAAATATTAAT-ATT
4208343 T--AA-ATT-AT-TT
1 TAAAATATTAATATT
4208353 TAAAATATTAATATT
1 TAAAATATTAATATT
*
4208368 TAAATTATTAAT
1 TAAAATATTAAT
4208380 TATTAATAGT
Statistics
Matches: 43, Mismatches: 2, Indels: 14
0.73 0.03 0.24
Matches are distributed among these distances:
10 2 0.05
11 2 0.05
12 5 0.12
13 5 0.12
14 2 0.05
15 26 0.60
16 1 0.02
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (15 bp):
TAAAATATTAATATT
Found at i:4208358 original size:25 final size:25
Alignment explanation
Indices: 4208326--4208376 Score: 86
Period size: 25 Copynumber: 2.0 Consensus size: 25
4208316 AATATTAGTA
4208326 TTTAAAATATTAATGA-TTAAATTAT
1 TTTAAAATATTAAT-ATTTAAATTAT
4208351 TTTAAAATATTAATATTTAAATTAT
1 TTTAAAATATTAATATTTAAATTAT
4208376 T
1 T
4208377 AATTATTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 1 0.04
25 24 0.96
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (25 bp):
TTTAAAATATTAATATTTAAATTAT
Found at i:4208368 original size:40 final size:40
Alignment explanation
Indices: 4208296--4208412 Score: 119
Period size: 40 Copynumber: 2.9 Consensus size: 40
4208286 TTAATCGTAA
*
4208296 TAATATTAAATTATAAATAAAATATTAGTATTTAAAATAT
1 TAATATTAAATTATAAATAAAATATTAATATTTAAAATAT
** *
4208336 TAATGATTAAATTAT-TTTAAAATATTAATATTTAAATTAT
1 TAAT-ATTAAATTATAAATAAAATATTAATATTTAAAATAT
* * * * *
4208376 TAATTATTAATAGTATAATTAAATTATAAATTTTTAA
1 TAA-TATTAA-ATTATAAATAAAATATTAATATTTAA
4208413 TATTTAAAAA
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
40 33 0.52
41 15 0.23
42 16 0.25
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (40 bp):
TAATATTAAATTATAAATAAAATATTAATATTTAAAATAT
Found at i:4208631 original size:43 final size:43
Alignment explanation
Indices: 4208577--4208682 Score: 194
Period size: 43 Copynumber: 2.5 Consensus size: 43
4208567 TACCAAAACA
4208577 ACGTAATAACTATTCTATTCTATTTTCATCTCATTCCATTCTT
1 ACGTAATAACTATTCTATTCTATTTTCATCTCATTCCATTCTT
*
4208620 ACGTAATAACTATTCTATTCTATTTTCATCTCATTCTATTCTT
1 ACGTAATAACTATTCTATTCTATTTTCATCTCATTCCATTCTT
*
4208663 ATGTAATAACTATTCTATTC
1 ACGTAATAACTATTCTATTC
4208683 CATTCCTATC
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
43 61 1.00
ACGTcount: A:0.27, C:0.21, G:0.03, T:0.49
Consensus pattern (43 bp):
ACGTAATAACTATTCTATTCTATTTTCATCTCATTCCATTCTT
Found at i:4208639 original size:22 final size:21
Alignment explanation
Indices: 4208579--4208682 Score: 63
Period size: 22 Copynumber: 4.9 Consensus size: 21
4208569 CCAAAACAAC
4208579 GTAATAACTATTCTATTC-TA
1 GTAATAACTATTCTATTCTTA
** * *
4208599 -TTTTCATCTCATTCCATTCTTA
1 GTAAT-AACT-ATTCTATTCTTA
4208621 CGTAATAACTATTCTATTC-TA
1 -GTAATAACTATTCTATTCTTA
** *
4208642 -TTTTCATCTCATTCTATTCTTA
1 GTAAT-AACT-ATTCTATTCTTA
4208664 TGTAATAACTATTCTATTC
1 -GTAATAACTATTCTATTC
4208683 CATTCCTATC
Statistics
Matches: 60, Mismatches: 14, Indels: 18
0.65 0.15 0.20
Matches are distributed among these distances:
19 4 0.07
20 6 0.10
21 19 0.32
22 21 0.35
23 6 0.10
24 4 0.07
ACGTcount: A:0.27, C:0.20, G:0.03, T:0.50
Consensus pattern (21 bp):
GTAATAACTATTCTATTCTTA
Found at i:4208848 original size:16 final size:17
Alignment explanation
Indices: 4208829--4208861 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
4208819 TTTCTCTTTT
4208829 AGAGTTT-TTGAGAAAA
1 AGAGTTTATTGAGAAAA
4208845 AGAGTTTGATTGAGAAA
1 AGAGTTT-ATTGAGAAA
4208862 GAAGGACAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.42, C:0.00, G:0.27, T:0.30
Consensus pattern (17 bp):
AGAGTTTATTGAGAAAA
Found at i:4222193 original size:46 final size:46
Alignment explanation
Indices: 4222126--4222217 Score: 157
Period size: 46 Copynumber: 2.0 Consensus size: 46
4222116 AACGAAATTC
*
4222126 TTAACTCTAACTATCTGAGAGATTCAAATTATTATTGATAGAAGTA
1 TTAACTCTAACCATCTGAGAGATTCAAATTATTATTGATAGAAGTA
* *
4222172 TTAACTCTAACCGTCTGAGAGATTCAACTTATTATTGATAGAAGTA
1 TTAACTCTAACCATCTGAGAGATTCAAATTATTATTGATAGAAGTA
4222218 CTTGTATACT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36
Consensus pattern (46 bp):
TTAACTCTAACCATCTGAGAGATTCAAATTATTATTGATAGAAGTA
Found at i:4229425 original size:12 final size:12
Alignment explanation
Indices: 4229408--4229443 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
4229398 TAAGGAAGGG
*
4229408 GAGAGAAATAGA
1 GAGAGAAACAGA
*
4229420 GAGAGAGACAGA
1 GAGAGAAACAGA
4229432 GAGAGAAACAGA
1 GAGAGAAACAGA
4229444 AGGACAGAGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.56, C:0.06, G:0.36, T:0.03
Consensus pattern (12 bp):
GAGAGAAACAGA
Found at i:4240779 original size:19 final size:19
Alignment explanation
Indices: 4240755--4240804 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
4240745 ATTGATGTCG
4240755 TTTACAATGCCCAAATATC
1 TTTACAATGCCCAAATATC
* *
4240774 TTTACAATCCCCAAATGTC
1 TTTACAATGCCCAAATATC
4240793 TTTACAATGCCC
1 TTTACAATGCCC
4240805 TAAAGTCAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.32, C:0.30, G:0.06, T:0.32
Consensus pattern (19 bp):
TTTACAATGCCCAAATATC
Found at i:4241773 original size:161 final size:161
Alignment explanation
Indices: 4241502--4241824 Score: 628
Period size: 161 Copynumber: 2.0 Consensus size: 161
4241492 AAAAACTACG
* *
4241502 TCAATTGAAGAATATACAATGGAGTTCGAAACAACTTTACACAAAGTGTGATGTCCATGAACTTG
1 TCAATGGAAGAATATACAATGGAGTTCGAAACAACTTTACACAAAGTGCGATGTCCATGAACTTG
4241567 AAAAACAAACTGTAGCTCGTTATCTTGGGGGTCTTAATGTTGAAATTATAGATGTTATTCATCTA
66 AAAAACAAACTGTAGCTCGTTATCTTGGGGGTCTTAATGTTGAAATTATAGATGTTATTCATCTA
4241632 AAACCATATTCGAACTTAAATGATGTTATCA
131 AAACCATATTCGAACTTAAATGATGTTATCA
4241663 TCAATGGAAGAATATACAATGGAGTTCGAAACAACTTTACACAAAGTGCGATGTCCATGAACTTG
1 TCAATGGAAGAATATACAATGGAGTTCGAAACAACTTTACACAAAGTGCGATGTCCATGAACTTG
4241728 AAAAACAAACTGTAGCTCGTTATCTTGGGGGTCTTAATGTTGAAATTATAGATGTTATTCATCTA
66 AAAAACAAACTGTAGCTCGTTATCTTGGGGGTCTTAATGTTGAAATTATAGATGTTATTCATCTA
4241793 AAACCATATTCGAACTTAAATGATGTTATCA
131 AAACCATATTCGAACTTAAATGATGTTATCA
4241824 T
1 T
4241825 ATTATCATTA
Statistics
Matches: 160, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
161 160 1.00
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.32
Consensus pattern (161 bp):
TCAATGGAAGAATATACAATGGAGTTCGAAACAACTTTACACAAAGTGCGATGTCCATGAACTTG
AAAAACAAACTGTAGCTCGTTATCTTGGGGGTCTTAATGTTGAAATTATAGATGTTATTCATCTA
AAACCATATTCGAACTTAAATGATGTTATCA
Found at i:4244043 original size:26 final size:26
Alignment explanation
Indices: 4244013--4244063 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
4244003 TTATTCTTTG
* *
4244013 TGTCTTCTTACCTAGCAGCCATCATT
1 TGTCTTCTTACATAGCAACCATCATT
4244039 TGTCTTCTTACATAGCAACCATCAT
1 TGTCTTCTTACATAGCAACCATCAT
4244064 GGTATTAAAG
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:0.24, C:0.29, G:0.10, T:0.37
Consensus pattern (26 bp):
TGTCTTCTTACATAGCAACCATCATT
Found at i:4250339 original size:18 final size:18
Alignment explanation
Indices: 4250316--4250354 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
4250306 ATTTAAGAAT
4250316 TAAATTTTAAATAA-AAAA
1 TAAA-TTTAAATAATAAAA
*
4250334 TAAATTTAATTAATAAAA
1 TAAATTTAAATAATAAAA
4250352 TAA
1 TAA
4250355 TTTCTCGAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
TAAATTTAAATAATAAAA
Found at i:4251796 original size:64 final size:64
Alignment explanation
Indices: 4251710--4251863 Score: 165
Period size: 64 Copynumber: 2.5 Consensus size: 64
4251700 TTTTGTGGAT
* * * * *
4251710 TTAAA-TATAACCTCTCTATCTTTTCAG-TCTTAGATAGAACCTTTAGATGATA-CTTTTTAAAA
1 TTAAAGTATAACTTCTCTATCTTTTAAGAT-TTAGATAGAACCTCTAAATAATATC-TTTTAAAA
4251772 G
64 G
* *
4251773 TTAAAGTATAACTTCTCTATCTTTTAAGATTTATATAGAACCTCTAAATAATATCTTTTGAAAG
1 TTAAAGTATAACTTCTCTATCTTTTAAGATTTAGATAGAACCTCTAAATAATATCTTTTAAAAG
* * *
4251837 TTAAGGTATAAGTTC-CTAT-TTTCAAGA
1 TTAAAGTATAACTTCTCTATCTTTTAAGA
4251864 ATTTGAATGT
Statistics
Matches: 78, Mismatches: 10, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
62 7 0.09
63 9 0.12
64 60 0.77
65 2 0.03
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.42
Consensus pattern (64 bp):
TTAAAGTATAACTTCTCTATCTTTTAAGATTTAGATAGAACCTCTAAATAATATCTTTTAAAAG
Found at i:4256410 original size:29 final size:28
Alignment explanation
Indices: 4256372--4256519 Score: 152
Period size: 29 Copynumber: 5.1 Consensus size: 28
4256362 AAGTTAATAA
*
4256372 AGAAAAGCTGTACGTGAACAGGTACAAG
1 AGAAAAGCTGTACATGAACAGGTACAAG
* * *
4256400 AGAGGAAGCTGTACATAAACAAGTACAAG
1 AGA-AAAGCTGTACATGAACAGGTACAAG
* *
4256429 AGAAAAGGCAGTACTTGAACAGGTACAAG
1 AGAAAA-GCTGTACATGAACAGGTACAAG
* *
4256458 AGAGGAAGCTGTACATAAACAGGTACAAG
1 AGA-AAAGCTGTACATGAACAGGTACAAG
* * * *
4256487 AGAAAAGGATGTACGTGAACAAGTATAAG
1 AGAAAA-GCTGTACATGAACAGGTACAAG
4256516 AGAA
1 AGAA
4256520 CAAGGAAAAA
Statistics
Matches: 97, Mismatches: 19, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
28 7 0.07
29 88 0.91
30 2 0.02
ACGTcount: A:0.47, C:0.12, G:0.27, T:0.14
Consensus pattern (28 bp):
AGAAAAGCTGTACATGAACAGGTACAAG
Found at i:4256461 original size:58 final size:58
Alignment explanation
Indices: 4256372--4256518 Score: 226
Period size: 58 Copynumber: 2.6 Consensus size: 58
4256362 AAGTTAATAA
*
4256372 AGAAAA-GCTGTACGTGAACAGGTACAAGAGAGGAAGCTGTACATAAACAAGTACAAG
1 AGAAAAGGCAGTACGTGAACAGGTACAAGAGAGGAAGCTGTACATAAACAAGTACAAG
* *
4256429 AGAAAAGGCAGTACTTGAACAGGTACAAGAGAGGAAGCTGTACATAAACAGGTACAAG
1 AGAAAAGGCAGTACGTGAACAGGTACAAGAGAGGAAGCTGTACATAAACAAGTACAAG
* *
4256487 AGAAAAGG-ATGTACGTGAACAAGTATAAGAGA
1 AGAAAAGGCA-GTACGTGAACAGGTACAAGAGA
4256519 ACAAGGAAAA
Statistics
Matches: 82, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
57 7 0.09
58 75 0.91
ACGTcount: A:0.46, C:0.12, G:0.27, T:0.14
Consensus pattern (58 bp):
AGAAAAGGCAGTACGTGAACAGGTACAAGAGAGGAAGCTGTACATAAACAAGTACAAG
Found at i:4259641 original size:128 final size:126
Alignment explanation
Indices: 4259435--4259671 Score: 307
Period size: 128 Copynumber: 1.9 Consensus size: 126
4259425 TTTATCCAGT
* * * *
4259435 TTTTATTATTTAGATTTTTATTATGTTTTTTTATAATGTTATTGCTTCTAAATAGAAATTAGAAA
1 TTTTATTAGTTAGATTTTTATTATGTTTTTTTATAATGTTATTGCTTCCAAATAGAAATCAAAAA
**
4259500 CCTTCCGTATAAGTTTCTAA-TTTCCTTTCTTCTTATCTCATTTTATTTGTTTATTCCAAC
66 CCTTAAGTATAAGTTTCTAATTTTCCTTTCTTCTTATCTCATTTTATTTGTTTATTCCAAC
* *
4259560 TTTTATTAGTTAGATTCTTTATTACTTTTATTTTTATAATGTTATTGCTTCCATATAGAAATCAA
1 TTTTATTAGTTAGATT-TTTATTA-TGTT-TTTTTATAATGTTATTGCTTCCAAATAGAAATCAA
* * * * *
4259625 AAAGCTTTAAG-GTAAGTTTCTAATTTTTCTTTCTTTTTATTTCATTT
63 AAA-CCTTAAGTATAAGTTTCTAATTTTCCTTTCTTCTTATCTCATTT
4259672 AATTAAATGT
Statistics
Matches: 94, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
125 15 0.16
126 7 0.07
127 3 0.03
128 45 0.48
129 24 0.26
ACGTcount: A:0.26, C:0.11, G:0.08, T:0.55
Consensus pattern (126 bp):
TTTTATTAGTTAGATTTTTATTATGTTTTTTTATAATGTTATTGCTTCCAAATAGAAATCAAAAA
CCTTAAGTATAAGTTTCTAATTTTCCTTTCTTCTTATCTCATTTTATTTGTTTATTCCAAC
Found at i:4267652 original size:285 final size:285
Alignment explanation
Indices: 4267142--4267997 Score: 1523
Period size: 285 Copynumber: 3.0 Consensus size: 285
4267132 ATGCCTTTGC
* *
4267142 CCTTATGACTTCGGTTGTTACTACCCTCTTCTGTAGATATGGTATTAACTTTGGAAACTGCTAAA
1 CCTTATGGCTTCGGTTGTTACTACCCTCTTCTGTAGATATGGTATTAACTTTGGAAGCTGCTAAA
*
4267207 TCCCTGGTGAGTTCATCCATTCGAGCATTTATTGCTTCTTGTCGAGCCAAATTGATTGCACATTC
66 TCCCTGGTGAGTTCATCCATTCGAGCATTTATTGCTTCTTGTCGAGCCAAATTGATTGCACGTTC
* *
4267272 ATCTTAAAACAATGGTAAAAGTTGCTGCAAAAGTTGTTGAATAGGGTCTCCCATAACATTAGGCT
131 ATCTTGAAACAATGGTAAAAGTTGCTGCAAAAGTTGCTGAATAGGGTCTCCCATAACATTAGGCT
* * **
4267337 TTGATACTAAATTGATACGGTTTCTTGAAACGGATCAAGTTATGGGACGGCGTATGGAAGGGTTT
196 CTGATACCAAATTGATACGGTCCCTTGAAACGGATCAAGTTATGGGACGGCGTATGGAAGGGTTT
4267402 AGTTTAGTTTGAGGTACACTACGTA
261 AGTTTAGTTTGAGGTACACTACGTA
4267427 CCTTATGGCTTCGGTTGTTACTACCCTCTTCTGTAGATATGGTATTAACTTTGGAAGCTGCTAAA
1 CCTTATGGCTTCGGTTGTTACTACCCTCTTCTGTAGATATGGTATTAACTTTGGAAGCTGCTAAA
* *
4267492 TCCTTGGTGAGTTCATCCATTCGAGCATTTATTGCTTCTTGTCGAGCCAAATTGATTGCACGTTT
66 TCCCTGGTGAGTTCATCCATTCGAGCATTTATTGCTTCTTGTCGAGCCAAATTGATTGCACGTTC
*
4267557 ATCTTGAAACAATGGTAAAAGTTGCTGCAAAAGTTGCTGAATAGAGTCTCCCATAACATTAGGCT
131 ATCTTGAAACAATGGTAAAAGTTGCTGCAAAAGTTGCTGAATAGGGTCTCCCATAACATTAGGCT
*
4267622 CTGATACCAAATTGATACGGTCCCTTGAAACGGATCAAGTTATGGGACGACGTATGGAAGGGTTT
196 CTGATACCAAATTGATACGGTCCCTTGAAACGGATCAAGTTATGGGACGGCGTATGGAAGGGTTT
4267687 AGTTTAGTTTGAGGTACACTACGTA
261 AGTTTAGTTTGAGGTACACTACGTA
4267712 CCTTATGGCTTCGGTTGTTACTACCCTCTTCTGTAGATATGGTATTAACTTTGGAAGCTGCTAAA
1 CCTTATGGCTTCGGTTGTTACTACCCTCTTCTGTAGATATGGTATTAACTTTGGAAGCTGCTAAA
* *
4267777 TCCCTGGTGAGTTCATCCATTCGAACATTTATTGCTTCTTGTCGAGCCAAATTGGTTGCACGTTC
66 TCCCTGGTGAGTTCATCCATTCGAGCATTTATTGCTTCTTGTCGAGCCAAATTGATTGCACGTTC
*
4267842 ATCTTGGAACAATGGTAAAAGTTGCTGCAAAAGTTGCTGAATAGGGTCTCCCATAACATTAGGCT
131 ATCTTGAAACAATGGTAAAAGTTGCTGCAAAAGTTGCTGAATAGGGTCTCCCATAACATTAGGCT
* * * *
4267907 CTGATACCAAATTGATACGGTCCTTTAAAATGGATCAAGTTATGAGACGGCGTATGGAAGGGTTT
196 CTGATACCAAATTGATACGGTCCCTTGAAACGGATCAAGTTATGGGACGGCGTATGGAAGGGTTT
*
4267972 AGTTTAGTTTGAGATACACTACGTA
261 AGTTTAGTTTGAGGTACACTACGTA
4267997 C
1 C
4267998 TTGGGTTGAT
Statistics
Matches: 546, Mismatches: 25, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
285 546 1.00
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.34
Consensus pattern (285 bp):
CCTTATGGCTTCGGTTGTTACTACCCTCTTCTGTAGATATGGTATTAACTTTGGAAGCTGCTAAA
TCCCTGGTGAGTTCATCCATTCGAGCATTTATTGCTTCTTGTCGAGCCAAATTGATTGCACGTTC
ATCTTGAAACAATGGTAAAAGTTGCTGCAAAAGTTGCTGAATAGGGTCTCCCATAACATTAGGCT
CTGATACCAAATTGATACGGTCCCTTGAAACGGATCAAGTTATGGGACGGCGTATGGAAGGGTTT
AGTTTAGTTTGAGGTACACTACGTA
Found at i:4270336 original size:13 final size:13
Alignment explanation
Indices: 4270318--4270344 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
4270308 CAAGAACCCA
4270318 AGAAAACTAACTT
1 AGAAAACTAACTT
4270331 AGAAAACTAACTT
1 AGAAAACTAACTT
4270344 A
1 A
4270345 TACGTTAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.15, G:0.07, T:0.22
Consensus pattern (13 bp):
AGAAAACTAACTT
Found at i:4278411 original size:10 final size:10
Alignment explanation
Indices: 4278393--4278436 Score: 61
Period size: 10 Copynumber: 4.2 Consensus size: 10
4278383 ATTGGACCAT
4278393 TCTCACTTTC
1 TCTCACTTTC
*
4278403 TCTCTCTTTC
1 TCTCACTTTC
4278413 TCCTTCACTTTC
1 T-C-TCACTTTC
4278425 TCTCACTTTC
1 TCTCACTTTC
4278435 TC
1 TC
4278437 GAGGAAAATC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
10 20 0.67
11 2 0.07
12 8 0.27
ACGTcount: A:0.07, C:0.41, G:0.00, T:0.52
Consensus pattern (10 bp):
TCTCACTTTC
Found at i:4278423 original size:22 final size:22
Alignment explanation
Indices: 4278395--4278436 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
4278385 TGGACCATTC
*
4278395 TCACTTTCTCTCTCTTTCTCCT
1 TCACTTTCTCTCACTTTCTCCT
4278417 TCACTTTCTCTCACTTTCTC
1 TCACTTTCTCTCACTTTCTC
4278437 GAGGAAAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.07, C:0.40, G:0.00, T:0.52
Consensus pattern (22 bp):
TCACTTTCTCTCACTTTCTCCT
Found at i:4283874 original size:16 final size:17
Alignment explanation
Indices: 4283853--4283887 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
4283843 TTTCAAAGTA
4283853 TTTAAAA-ATAAATATT
1 TTTAAAATATAAATATT
4283869 TTTAAAATTATAAATATT
1 TTTAAAA-TATAAATATT
4283887 T
1 T
4283888 ATTTTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
18 10 0.59
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TTTAAAATATAAATATT
Found at i:4293001 original size:24 final size:25
Alignment explanation
Indices: 4292956--4293003 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
4292946 AAATAGTATT
4292956 TTAATTAATAATAATTAATTAATTA
1 TTAATTAATAATAATTAATTAATTA
*
4292981 TTAATT-ATAA-AATTTATTTAATT
1 TTAATTAATAATAA-TTAATTAATT
4293004 TAAAATAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 2 0.10
24 13 0.62
25 6 0.29
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
TTAATTAATAATAATTAATTAATTA
Found at i:4293049 original size:27 final size:29
Alignment explanation
Indices: 4292986--4293058 Score: 87
Period size: 30 Copynumber: 2.6 Consensus size: 29
4292976 AATTATTAAT
* *
4292986 TATAAAATTTATTTAATTTAAAATAAAAA
1 TATAAAATTTATTAAATGTAAAATAAAAA
* *
4293015 TATAAAAATTTATTAAATGTAACA-AAAGA
1 TAT-AAAATTTATTAAATGTAAAATAAAAA
4293044 -ATAAAATTTATTAAA
1 TATAAAATTTATTAAA
4293059 AAAAATTTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
27 13 0.33
28 2 0.05
29 7 0.18
30 17 0.44
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.37
Consensus pattern (29 bp):
TATAAAATTTATTAAATGTAAAATAAAAA
Found at i:4303616 original size:10 final size:10
Alignment explanation
Indices: 4303583--4303624 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
4303573 ATATAATATT
4303583 TTTAAAAAAA
1 TTTAAAAAAA
* **
4303593 TTT-TAATTA
1 TTTAAAAAAA
4303602 TTTAAAAAAA
1 TTTAAAAAAA
4303612 TTTAAAAAAA
1 TTTAAAAAAA
4303622 TTT
1 TTT
4303625 TTATTTTTTA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
9 6 0.24
10 19 0.76
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (10 bp):
TTTAAAAAAA
Found at i:4304162 original size:26 final size:27
Alignment explanation
Indices: 4304100--4304162 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 27
4304090 GCGCCCAAAA
* *
4304100 GCGTTCCAAACTCAAAAGCACCCATGG
1 GCGTTCCAAGCGCAAAAGCACCCATGG
* *
4304127 GCGTTCCAAGCGCAAAAGTATCCA-GG
1 GCGTTCCAAGCGCAAAAGCACCCATGG
*
4304153 GTGTTCCAAG
1 GCGTTCCAAG
4304163 TACAAAAACA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
26 11 0.35
27 20 0.65
ACGTcount: A:0.30, C:0.29, G:0.24, T:0.17
Consensus pattern (27 bp):
GCGTTCCAAGCGCAAAAGCACCCATGG
Found at i:4305433 original size:2 final size:2
Alignment explanation
Indices: 4305426--4305456 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4305416 TGCCTCACAA
4305426 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4305457 ACAAAAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4309303 original size:18 final size:18
Alignment explanation
Indices: 4309259--4309310 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
4309249 ATTAATAATT
* **
4309259 ATAATTAATATATAAAAA
1 ATAATTAATGTATTTAAA
4309277 ATAAATTAATGTATTTAAA
1 AT-AATTAATGTATTTAAA
*
4309296 ATAATTAATGAATTT
1 ATAATTAATGTATTT
4309311 TAATAAATAC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
18 14 0.48
19 15 0.52
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (18 bp):
ATAATTAATGTATTTAAA
Found at i:4309313 original size:19 final size:19
Alignment explanation
Indices: 4309274--4309310 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
4309264 TAATATATAA
*
4309274 AAAATAAATTAATGTATTT
1 AAAATAAATTAATGAATTT
4309293 AAAAT-AATTAATGAATTT
1 AAAATAAATTAATGAATTT
4309311 TAATAAATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (19 bp):
AAAATAAATTAATGAATTT
Found at i:4314517 original size:26 final size:26
Alignment explanation
Indices: 4314484--4314536 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
4314474 TCATTGTCCC
* *
4314484 AAAAGAAATGATACGCGTGGAGACAA
1 AAAAGAAATGATAAGCATGGAGACAA
4314510 AAAAGAAATGATAAGCATGGAGACAA
1 AAAAGAAATGATAAGCATGGAGACAA
4314536 A
1 A
4314537 GGCAAAGATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.55, C:0.09, G:0.25, T:0.11
Consensus pattern (26 bp):
AAAAGAAATGATAAGCATGGAGACAA
Found at i:4317562 original size:3 final size:3
Alignment explanation
Indices: 4317556--4317581 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
4317546 TTTTTCATTA
4317556 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
4317582 AACTGTGACA
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:4318300 original size:2 final size:2
Alignment explanation
Indices: 4318293--4318323 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4318283 TTGAGGGTCC
4318293 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4318324 TAAGTAGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4325214 original size:24 final size:23
Alignment explanation
Indices: 4325173--4325226 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
4325163 AAATTTTGTT
* *
4325173 GAAATTCTGTTGGAAATCTATAA
1 GAAATTTTGTTGGAAATCCATAA
* *
4325196 GAAATTTTCGTTGGCAATCCATAG
1 GAAATTTT-GTTGGAAATCCATAA
4325220 GAAATTT
1 GAAATTT
4325227 CCATTGAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
23 7 0.27
24 19 0.73
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.35
Consensus pattern (23 bp):
GAAATTTTGTTGGAAATCCATAA
Found at i:4329189 original size:107 final size:108
Alignment explanation
Indices: 4328988--4329192 Score: 322
Period size: 107 Copynumber: 1.9 Consensus size: 108
4328978 TGAAATGACT
* * * * * *
4328988 AAATATGTTGATTTTGTTACAACTTTCATAATTTACAAATATACATTCTTTTGAAATTATTCAAC
1 AAATATGTTGAATTAGTTACAACTTTCACAATTTACAAATACACATTCGTTTCAAATTATTCAAC
4329053 TCTTACACAATTTACCTTTTATTTAAATTTACTTAAATTAACA
66 TCTTACACAATTTACCTTTTATTTAAATTTACTTAAATTAACA
* *
4329096 AAATATGTT-AATTAGTTACAACTTTCACAATTTATAAATACACGTTCGTTTCAAATTATTCAAC
1 AAATATGTTGAATTAGTTACAACTTTCACAATTTACAAATACACATTCGTTTCAAATTATTCAAC
*
4329160 TCTTACCCAATTTACCTTTTATTTAAATTTACT
66 TCTTACACAATTTACCTTTTATTTAAATTTACT
4329193 CAAACTTTCT
Statistics
Matches: 88, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
107 79 0.90
108 9 0.10
ACGTcount: A:0.36, C:0.16, G:0.04, T:0.44
Consensus pattern (108 bp):
AAATATGTTGAATTAGTTACAACTTTCACAATTTACAAATACACATTCGTTTCAAATTATTCAAC
TCTTACACAATTTACCTTTTATTTAAATTTACTTAAATTAACA
Found at i:4340962 original size:30 final size:30
Alignment explanation
Indices: 4340928--4341010 Score: 150
Period size: 30 Copynumber: 2.8 Consensus size: 30
4340918 TAACTTTGAT
4340928 AAATATTAATATTTAACTTAAAATATTAAA
1 AAATATTAATATTTAACTTAAAATATTAAA
4340958 AAATATTAATATTTAACTTAAAATATTAAA
1 AAATATTAATATTTAACTTAAAATATTAAA
*
4340988 AAATATTAATATTT-AGTTAAAAT
1 AAATATTAATATTTAACTTAAAAT
4341011 TTTTAACTTA
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
29 8 0.15
30 44 0.85
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.41
Consensus pattern (30 bp):
AAATATTAATATTTAACTTAAAATATTAAA
Found at i:4340970 original size:16 final size:16
Alignment explanation
Indices: 4340949--4341000 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 16
4340939 TTTAACTTAA
4340949 AATATTAAAAAATATT
1 AATATTAAAAAATATT
* ** *
4340965 AATATT-TAACTTA-A
1 AATATTAAAAAATATT
4340979 AATATTAAAAAATATT
1 AATATTAAAAAATATT
4340995 AATATT
1 AATATT
4341001 TAGTTAAAAT
Statistics
Matches: 26, Mismatches: 8, Indels: 4
0.68 0.21 0.11
Matches are distributed among these distances:
14 6 0.23
15 8 0.31
16 12 0.46
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (16 bp):
AATATTAAAAAATATT
Found at i:4344350 original size:22 final size:22
Alignment explanation
Indices: 4344298--4344344 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
4344288 ATAATTTTAA
*
4344298 TTAATTTAATAATTTTATATAT
1 TTAATTAAATAATTTTATATAT
4344320 TTAATTAAATAATTTTATATAT
1 TTAATTAAATAATTTTATATAT
4344342 TTA
1 TTA
4344345 TATAAAATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TTAATTAAATAATTTTATATAT
Found at i:4345392 original size:27 final size:30
Alignment explanation
Indices: 4345320--4345393 Score: 86
Period size: 29 Copynumber: 2.6 Consensus size: 30
4345310 AATTATTAGT
* *
4345320 TATAAAAGC-TTATTTGAATAAAATAAAAA
1 TATAAGAGCTTTATTTGAAGAAAATAAAAA
*
4345349 TATAAGAGCTTTA-TTGAAGACAAT-AAAA
1 TATAAGAGCTTTATTTGAAGAAAATAAAAA
4345377 -ATAAGAG-TTTATTTGAA
1 TATAAGAGCTTTATTTGAA
4345394 TTTTTTTGAA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
26 4 0.10
27 12 0.30
28 4 0.10
29 17 0.43
30 3 0.08
ACGTcount: A:0.51, C:0.04, G:0.12, T:0.32
Consensus pattern (30 bp):
TATAAGAGCTTTATTTGAAGAAAATAAAAA
Found at i:4348546 original size:169 final size:170
Alignment explanation
Indices: 4348264--4348618 Score: 491
Period size: 169 Copynumber: 2.1 Consensus size: 170
4348254 ATGATTTGAT
* * * *
4348264 GCTAGAATTAAACATTAAGAATTATGTTGAGGAATTAATGTTTAGAATTATTGTTTTTGTTTTTA
1 GCTAGAATTAAACATTAAAAATTATGTTGAGAAATTAATGTTTAGAATTATTGATTTAGTTTTTA
* * * * *
4348329 ATTTAAACGATGGGTAATAAATTAGGATTAAACATTAATAATTATGTTTGGGAATTAATG-TTAA
66 ATTAAAACGATGGGCAATAAATTAGAATTAAACATTAAAAACTATGTTTGGGAATTAATGTTTAA
*
4348393 AATTATTGTTTAGATTTTTAATTAAAATGATTGGTAATAC
131 AATTATTATTTAGATTTTTAATTAAAATGATTGGTAATAC
*
4348433 GCTAGAATTAAATATTAAAAATTATGTTTGA-AAATTAATGTTTAGAATTATT-ATTTAGATTTT
1 GCTAGAATTAAACATTAAAAATTATG-TTGAGAAATTAATGTTTAGAATTATTGATTTAG-TTTT
* * ** *
4348496 TAATTAAAATGATTGGCAATATGTTAGAATTAAATATTAAAAACTATGTTTGGGAATTAATGTTT
64 TAATTAAAACGATGGGCAATAAATTAGAATTAAACATTAAAAACTATGTTTGGGAATTAATGTTT
* * *
4348561 AGAATTATTATTTCGATTTTTAATTAAAATGATTGGTAATAT
129 AAAATTATTATTTAGATTTTTAATTAAAATGATTGGTAATAC
*
4348603 ACTAGAATTAAACATT
1 GCTAGAATTAAACATT
4348619 GGAATTAATA
Statistics
Matches: 162, Mismatches: 21, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
168 4 0.02
169 100 0.62
170 58 0.36
ACGTcount: A:0.40, C:0.03, G:0.14, T:0.43
Consensus pattern (170 bp):
GCTAGAATTAAACATTAAAAATTATGTTGAGAAATTAATGTTTAGAATTATTGATTTAGTTTTTA
ATTAAAACGATGGGCAATAAATTAGAATTAAACATTAAAAACTATGTTTGGGAATTAATGTTTAA
AATTATTATTTAGATTTTTAATTAAAATGATTGGTAATAC
Found at i:4348633 original size:85 final size:85
Alignment explanation
Indices: 4348265--4348618 Score: 462
Period size: 85 Copynumber: 4.2 Consensus size: 85
4348255 TGATTTGATG
* * *
4348265 CTAGAATTAAACATTAAGAATTATG-TTGAGGAATTAATGTTTAGAATTATTGTTTTTG-TTTTT
1 CTAGAATTAAACATTAAAAATTATGTTTG-GGAATTAATGTTTAGAATTATT-ATTTAGATTTTT
* * * *
4348328 AATTTAAACGATGGGTAATAAA
64 AATTAAAATGATTGGTAATATA
* * * * *
4348350 TTAGGATTAAACATTAATAATTATGTTTGGGAATTAATG-TTAAAATTATTGTTTAGATTTTTAA
1 CTAGAATTAAACATTAAAAATTATGTTTGGGAATTAATGTTTAGAATTATTATTTAGATTTTTAA
**
4348414 TTAAAATGATTGGTAATACG
66 TTAAAATGATTGGTAATATA
* **
4348434 CTAGAATTAAATATTAAAAATTATGTTTGAAAATTAATGTTTAGAATTATTATTTAGATTTTTAA
1 CTAGAATTAAACATTAAAAATTATGTTTGGGAATTAATGTTTAGAATTATTATTTAGATTTTTAA
* *
4348499 TTAAAATGATTGGCAATATG
66 TTAAAATGATTGGTAATATA
* * * *
4348519 TTAGAATTAAATATTAAAAACTATGTTTGGGAATTAATGTTTAGAATTATTATTTCGATTTTTAA
1 CTAGAATTAAACATTAAAAATTATGTTTGGGAATTAATGTTTAGAATTATTATTTAGATTTTTAA
4348584 TTAAAATGATTGGTAATATA
66 TTAAAATGATTGGTAATATA
4348604 CTAGAATTAAACATT
1 CTAGAATTAAACATT
4348619 GGAATTAATA
Statistics
Matches: 236, Mismatches: 30, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
83 4 0.02
84 65 0.28
85 164 0.69
86 3 0.01
ACGTcount: A:0.40, C:0.03, G:0.14, T:0.43
Consensus pattern (85 bp):
CTAGAATTAAACATTAAAAATTATGTTTGGGAATTAATGTTTAGAATTATTATTTAGATTTTTAA
TTAAAATGATTGGTAATATA
Found at i:4350255 original size:12 final size:12
Alignment explanation
Indices: 4350238--4350262 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4350228 GAAGTGACTG
4350238 AAAGATAATTAT
1 AAAGATAATTAT
4350250 AAAGATAATTAT
1 AAAGATAATTAT
4350262 A
1 A
4350263 CTATATATAT
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:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (12 bp):
AAAGATAATTAT
Found at i:4362540 original size:17 final size:18
Alignment explanation
Indices: 4362515--4362548 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
4362505 TTATAGTATT
*
4362515 AATTTATAAAT-TATTTC
1 AATTGATAAATATATTTC
4362532 AATTGATAAATATATTT
1 AATTGATAAATATATTT
4362549 TTAATAAAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (18 bp):
AATTGATAAATATATTTC
Found at i:4362747 original size:9 final size:10
Alignment explanation
Indices: 4362707--4362752 Score: 51
Period size: 9 Copynumber: 4.6 Consensus size: 10
4362697 ATATTTTTAT
*
4362707 ATATATCATA
1 ATATATAATA
4362717 A-ATATATATAA
1 ATATATA-AT-A
4362728 ATATATAATA
1 ATATATAATA
4362738 ATAT-TAATA
1 ATATATAATA
4362747 ATATAT
1 ATATAT
4362753 GTATGTATGT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
9 13 0.42
10 9 0.29
11 4 0.13
12 5 0.16
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (10 bp):
ATATATAATA
Found at i:4362752 original size:21 final size:22
Alignment explanation
Indices: 4362705--4362752 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
4362695 TTATATTTTT
*
4362705 ATATATATCATAAATATATATA
1 ATATATATAATAAATATATATA
4362727 A-ATATATAAT-AATAT-TAATA
1 ATATATATAATAAATATAT-ATA
4362747 ATATAT
1 ATATAT
4362753 GTATGTATGT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
19 1 0.04
20 9 0.39
21 12 0.52
22 1 0.04
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (22 bp):
ATATATATAATAAATATATATA
Found at i:4364004 original size:14 final size:14
Alignment explanation
Indices: 4363959--4364029 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 14
4363949 ATTAAACATA
4363959 AAATTAACTAAGTTT
1 AAATTAACTAA-TTT
* * **
4363974 AAATTGACTCACCT
1 AAATTAACTAATTT
4363988 AAATTAACTAATTT
1 AAATTAACTAATTT
* * * *
4364002 AAAATAATTAAATA
1 AAATTAACTAATTT
*
4364016 AAATTTACTAATTT
1 AAATTAACTAATTT
4364030 CTATGTATCA
Statistics
Matches: 39, Mismatches: 17, Indels: 1
0.68 0.30 0.02
Matches are distributed among these distances:
14 30 0.77
15 9 0.23
ACGTcount: A:0.49, C:0.10, G:0.03, T:0.38
Consensus pattern (14 bp):
AAATTAACTAATTT
Found at i:4366739 original size:36 final size:36
Alignment explanation
Indices: 4366688--4366769 Score: 101
Period size: 36 Copynumber: 2.3 Consensus size: 36
4366678 AGTCATGTGA
* * *
4366688 ACTCCCACACTGCACATAGCAATTATCATCATATGC
1 ACTCCCACACCGCACATAACAATTATCACCATATGC
* ** *
4366724 ACTCCCACACCGCACATAACTATTATTGCCATGTGC
1 ACTCCCACACCGCACATAACAATTATCACCATATGC
4366760 ACTCCCACAC
1 ACTCCCACAC
4366770 AACACATGGT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.30, C:0.38, G:0.09, T:0.23
Consensus pattern (36 bp):
ACTCCCACACCGCACATAACAATTATCACCATATGC
Found at i:4372608 original size:15 final size:14
Alignment explanation
Indices: 4372574--4372614 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
4372564 GTTTTTAATT
4372574 ATTTATATTTTATA
1 ATTTATATTTTATA
*
4372588 AATTATAATTTTAT-
1 ATTTAT-ATTTTATA
4372602 ATTT-TATTTTATA
1 ATTTATATTTTATA
4372615 TTTTTATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
12 7 0.30
13 1 0.04
14 8 0.35
15 7 0.30
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
ATTTATATTTTATA
Found at i:4376453 original size:29 final size:28
Alignment explanation
Indices: 4376409--4376498 Score: 108
Period size: 29 Copynumber: 3.1 Consensus size: 28
4376399 TTGTTCTTTG
* * *
4376409 TTCTCTTATACTTGTTCAGGTACAGCCTT
1 TTCTCTTGTACCTGTTCACGTACAG-CTT
*
4376438 TTCTCTTGTACCTGTTCATGTACAGCTT
1 TTCTCTTGTACCTGTTCACGTACAGCTT
* *
4376466 CCTCTCTTGTACCTGTTCACGTACGGCTT
1 -TTCTCTTGTACCTGTTCACGTACAGCTT
4376495 TTCT
1 TTCT
4376499 TTATTAATTC
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
28 6 0.11
29 47 0.89
ACGTcount: A:0.13, C:0.28, G:0.14, T:0.44
Consensus pattern (28 bp):
TTCTCTTGTACCTGTTCACGTACAGCTT
Found at i:4378826 original size:87 final size:88
Alignment explanation
Indices: 4378537--4378853 Score: 501
Period size: 88 Copynumber: 3.6 Consensus size: 88
4378527 TCTTGACTGC
* * *
4378537 AATTATATTATATTATTGGTCACAAGCTATATCGCTCAATCTTTAACCATAATTCAGCCACTAGC
1 AATTATATTACATTATTGGTCACAAGCTATATCGCTCAATCTTTGACCATAATTCAGCCGCTAGC
*
4378602 TTTATCGCTCATAATTTGGCTGT
66 TTTATCGCTCATGATTTGGCTGT
** * *
4378625 AATTATATTACATTATTGGTCGTAAGCTATATCACTCAATCTTTGACCATAATTCAGCCGCTAGT
1 AATTATATTACATTATTGGTCACAAGCTATATCGCTCAATCTTTGACCATAATTCAGCCGCTAGC
*
4378690 TTTATCGTTCATGATTTGGCTGT
66 TTTATCGCTCATGATTTGGCTGT
4378713 AATTATATTACATTATTGGTCACAAGCTATATCGCTCAATCTTTGACCATAATTCAG-CGCTAGC
1 AATTATATTACATTATTGGTCACAAGCTATATCGCTCAATCTTTGACCATAATTCAGCCGCTAGC
* *
4378777 TTTATCGCTCGTGATTTTGCTGT
66 TTTATCGCTCATGATTTGGCTGT
* * *
4378800 AATGATATTATATTATTGGTCGCAAGCTATATCGCTCAATCTTTGACCATAATT
1 AATTATATTACATTATTGGTCACAAGCTATATCGCTCAATCTTTGACCATAATT
4378854 TATCATTAAT
Statistics
Matches: 210, Mismatches: 19, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
87 77 0.37
88 133 0.63
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (88 bp):
AATTATATTACATTATTGGTCACAAGCTATATCGCTCAATCTTTGACCATAATTCAGCCGCTAGC
TTTATCGCTCATGATTTGGCTGT
Found at i:4378845 original size:175 final size:176
Alignment explanation
Indices: 4378537--4378853 Score: 537
Period size: 175 Copynumber: 1.8 Consensus size: 176
4378527 TCTTGACTGC
*
4378537 AATTATATTATATTATTGGTCACAAGCTATATCGCTCAATCTTTAACCATAATTCAGCCACTAGC
1 AATTATATTACATTATTGGTCACAAGCTATATCGCTCAATCTTTAACCATAATTCAGCCACTAGC
* *
4378602 TTTATCGCTCATAATTTGGCTGTAATTATATTACATTATTGGTCGTAAGCTATATCACTCAATCT
66 TTTATCGCTCATAATTTGGCTGTAATGATATTACATTATTGGTCGCAAGCTATATCACTCAATCT
4378667 TTGACCATAATTCAGCCGCTAGTTTTATCGTTCATGATTTGGCTGT
131 TTGACCATAATTCAGCCGCTAGTTTTATCGTTCATGATTTGGCTGT
* *
4378713 AATTATATTACATTATTGGTCACAAGCTATATCGCTCAATCTTTGACCATAATTCAG-CGCTAGC
1 AATTATATTACATTATTGGTCACAAGCTATATCGCTCAATCTTTAACCATAATTCAGCCACTAGC
* * * * *
4378777 TTTATCGCTCGTGATTTTGCTGTAATGATATTATATTATTGGTCGCAAGCTATATCGCTCAATCT
66 TTTATCGCTCATAATTTGGCTGTAATGATATTACATTATTGGTCGCAAGCTATATCACTCAATCT
4378842 TTGACCATAATT
131 TTGACCATAATT
4378854 TATCATTAAT
Statistics
Matches: 131, Mismatches: 10, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
175 76 0.58
176 55 0.42
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (176 bp):
AATTATATTACATTATTGGTCACAAGCTATATCGCTCAATCTTTAACCATAATTCAGCCACTAGC
TTTATCGCTCATAATTTGGCTGTAATGATATTACATTATTGGTCGCAAGCTATATCACTCAATCT
TTGACCATAATTCAGCCGCTAGTTTTATCGTTCATGATTTGGCTGT
Done.