Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 12 of 226
Found at i:5618844 original size:18 final size:19
Alignment explanation
Indices: 5618821--5618862 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
5618811 AATTTGCAGC
5618821 AAAAATATT-TTAAATTAA
1 AAAAATATTGTTAAATTAA
* *
5618839 AAAAATGTTGTTGAATTAA
1 AAAAATATTGTTAAATTAA
5618858 AAAAA
1 AAAAA
5618863 AAGATAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (19 bp):
AAAAATATTGTTAAATTAA
Found at i:5623781 original size:3 final size:3
Alignment explanation
Indices: 5623773--5623799 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
5623763 AACTGAAGAA
5623773 ATC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC
5623800 TTCTTGTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
ATC
Found at i:5631276 original size:23 final size:21
Alignment explanation
Indices: 5631231--5631288 Score: 73
Period size: 21 Copynumber: 2.7 Consensus size: 21
5631221 AGGTTACTGC
*
5631231 TTTTTGATGTTGTTTTCATTA
1 TTTTTGTTGTTGTTTTCATTA
5631252 TTTTTGTTGTTGTTATGTCATTA
1 TTTTTGTTGTTGTT-T-TCATTA
*
5631275 -TTTTGTTGTGGTTT
1 TTTTTGTTGTTGTTT
5631289 CGTTATTATA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.42
22 13 0.39
23 6 0.18
ACGTcount: A:0.10, C:0.03, G:0.19, T:0.67
Consensus pattern (21 bp):
TTTTTGTTGTTGTTTTCATTA
Found at i:5633531 original size:2 final size:2
Alignment explanation
Indices: 5633526--5633552 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5633516 TTTTTCATCT
5633526 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 T
5633553 TTGTTTTAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5650255 original size:18 final size:18
Alignment explanation
Indices: 5650234--5650278 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
5650224 CATTCTTCTC
5650234 CCCTTTCCCCTTCTCCTT
1 CCCTTTCCCCTTCTCCTT
5650252 CCCTTTCCCCTTCTCCTT
1 CCCTTTCCCCTTCTCCTT
5650270 CCCTTTCCC
1 CCCTTTCCC
5650279 GTTTCGAAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.00, C:0.58, G:0.00, T:0.42
Consensus pattern (18 bp):
CCCTTTCCCCTTCTCCTT
Found at i:5651459 original size:34 final size:35
Alignment explanation
Indices: 5651402--5651467 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 35
5651392 TAAACACCAG
* *
5651402 AAAATATTTTCCAGTAAGTCATTTTACAGAAATGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAATGT
* *
5651437 AAAACATTTTCTAG-AAATCATTTTACGGAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAA
5651468 ATATTTTACT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
34 15 0.56
35 12 0.44
ACGTcount: A:0.42, C:0.12, G:0.11, T:0.35
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAATGT
Found at i:5656877 original size:5 final size:5
Alignment explanation
Indices: 5656863--5656894 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
5656853 CTTTGAATAC
5656863 AAAA- AAAAG AAAAG AAAAG AAAAG AAAAG AAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAA
5656895 TGGGAATCTC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:5661608 original size:31 final size:31
Alignment explanation
Indices: 5661570--5661709 Score: 153
Period size: 31 Copynumber: 4.5 Consensus size: 31
5661560 TTAATATAAC
*
5661570 ATTTGGTACCTGAACTTGACACTTTTTCCTA
1 ATTTGGTACCTAAACTTGACACTTTTTCCTA
* **
5661601 ATTTGGTACTTAAACTT---TTTTTTGGTCC-A
1 ATTTGGTACCTAAACTTGACACTTTT--TCCTA
*
5661630 ATTTGGTATCTAAACTTGACACTTTTTTCCTA
1 ATTTGGTACCTAAACTTGACAC-TTTTTCCTA
*
5661662 ATTTGGTACCTAAACTTGACACTTTTTCTTA
1 ATTTGGTACCTAAACTTGACACTTTTTCCTA
* *
5661693 AGTTGGTACTTAAACTT
1 ATTTGGTACCTAAACTT
5661710 TTGGGGGTGC
Statistics
Matches: 90, Mismatches: 12, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
28 4 0.04
29 16 0.18
30 3 0.03
31 41 0.46
32 22 0.24
33 4 0.04
ACGTcount: A:0.24, C:0.18, G:0.12, T:0.46
Consensus pattern (31 bp):
ATTTGGTACCTAAACTTGACACTTTTTCCTA
Found at i:5671517 original size:17 final size:17
Alignment explanation
Indices: 5671495--5671533 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
5671485 TTTTTTTTCC
5671495 CTTCCCACCAACTCTTT
1 CTTCCCACCAACTCTTT
5671512 CTTCCCACCAACTCTTT
1 CTTCCCACCAACTCTTT
5671529 CTTCC
1 CTTCC
5671534 TTTCTTCTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.15, C:0.49, G:0.00, T:0.36
Consensus pattern (17 bp):
CTTCCCACCAACTCTTT
Found at i:5683011 original size:16 final size:16
Alignment explanation
Indices: 5682990--5683026 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
5682980 TCGCTTCGTT
*
5682990 GTAATGGAATAGAGGC
1 GTAATGAAATAGAGGC
5683006 GTAATGAAATAGAGGC
1 GTAATGAAATAGAGGC
5683022 GTAAT
1 GTAAT
5683027 AGCAAATCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.41, C:0.05, G:0.32, T:0.22
Consensus pattern (16 bp):
GTAATGAAATAGAGGC
Found at i:5683280 original size:18 final size:17
Alignment explanation
Indices: 5683259--5683293 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
5683249 TTATTATTAA
5683259 ATATAATTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
*
5683277 ATATGATTTAATAAAAT
1 ATATAATTTAATAAAAT
5683294 TTAAAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:5683307 original size:28 final size:27
Alignment explanation
Indices: 5683239--5683307 Score: 63
Period size: 28 Copynumber: 2.6 Consensus size: 27
5683229 TTAATCATAT
* *
5683239 TTTAACATAATTAT-TATTAAATATAA
1 TTTAAAATAATTATATATTAAATAAAA
*
5683265 TTTAATTAA-AA-TATATGATTTAATAAAA
1 TTTAA--AATAATTATAT-ATTAAATAAAA
5683293 TTTAAAATAATTATA
1 TTTAAAATAATTATA
5683308 ACTAATAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
26 10 0.29
27 5 0.15
28 19 0.56
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (27 bp):
TTTAAAATAATTATATATTAAATAAAA
Found at i:5683428 original size:47 final size:46
Alignment explanation
Indices: 5683276--5683434 Score: 143
Period size: 47 Copynumber: 3.5 Consensus size: 46
5683266 TTAATTAAAA
* *
5683276 TATATG-ATTTAATAAAATTTAAAATAATTATAACTAATAAATTTTCT
1 TATATGAATTT-ATATAATTTAAAATAATTATTA-TAATAAATTTTCT
* *
5683323 TATATGAATTTGTATAATTTAAAATAATTATTAT--TAAATATAAT-T
1 TATATGAATTTATATAATTTAAAATAATTATTATAATAAAT-T-TTCT
* * *
5683368 TA-AT-AATAATATATAATTTCATAA-AATTCTTGATAATAAATTTTCT
1 TATATGAAT-TTATATAATTT-AAAATAATTATT-ATAATAAATTTTCT
5683414 TATATGAATTTATATAATTTA
1 TATATGAATTTATATAATTTA
5683435 NNNNNNNNNN
Statistics
Matches: 91, Mismatches: 10, Indels: 23
0.73 0.08 0.19
Matches are distributed among these distances:
43 3 0.03
44 22 0.24
45 10 0.11
46 7 0.08
47 42 0.46
48 7 0.08
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (46 bp):
TATATGAATTTATATAATTTAAAATAATTATTATAATAAATTTTCT
Found at i:5686356 original size:14 final size:14
Alignment explanation
Indices: 5686337--5686371 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
5686327 ACTTTAAAAA
* *
5686337 TATTTTTATATTTT
1 TATTTTTAAAATTT
5686351 TATTTTTAAAATTT
1 TATTTTTAAAATTT
5686365 TATTTTT
1 TATTTTT
5686372 GTGTTTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TATTTTTAAAATTT
Found at i:5692789 original size:69 final size:69
Alignment explanation
Indices: 5692675--5692813 Score: 260
Period size: 69 Copynumber: 2.0 Consensus size: 69
5692665 CCCATTCCCC
*
5692675 TTTATTGTGTATCCACAAAATCTCATGAAATGGAAACTCGGAGTAGGCAATTCTATTTCTTTTCT
1 TTTATTGTGTATCCACAAAATCTCATGAAATGGAAACTCGAAGTAGGCAATTCTATTTCTTTTCT
5692740 TGTA
66 TGTA
*
5692744 TTTATTGTGTATCCGCAAAATCTCATGAAATGGAAACTCGAAGTAGGCAATTCTATTTCTTTTCT
1 TTTATTGTGTATCCACAAAATCTCATGAAATGGAAACTCGAAGTAGGCAATTCTATTTCTTTTCT
5692809 TGTA
66 TGTA
5692813 T
1 T
5692814 ACCCAATTTG
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 68 1.00
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.40
Consensus pattern (69 bp):
TTTATTGTGTATCCACAAAATCTCATGAAATGGAAACTCGAAGTAGGCAATTCTATTTCTTTTCT
TGTA
Found at i:5697893 original size:154 final size:154
Alignment explanation
Indices: 5697613--5697919 Score: 605
Period size: 154 Copynumber: 2.0 Consensus size: 154
5697603 TTGATAGACC
5697613 GTACAAAACAAATTGCTTATTACTTTAACCAATAATTGATATACTGATCCCGAACAACCATCGAC
1 GTACAAAACAAATTGCTTATTACTTTAACCAATAATTGATATACTGATCCCGAACAACCATCGAC
5697678 ATACAAAAGTTAATGCTGCCAACACCCCAACCACTCTGCATTATCAGAGAAGAAAGAACAGAGAG
66 ATACAAAAGTTAATGCTGCCAACACCCCAACCACTCTGCATTATCAGAGAAGAAAGAACAGAGAG
5697743 AAAGGTCCTAGATAGACATAGGCT
131 AAAGGTCCTAGATAGACATAGGCT
*
5697767 GTACAAAACAAATTGCTTATTACTTTAACCAATAATTGATATACTGATCCCGAACAACCATTGAC
1 GTACAAAACAAATTGCTTATTACTTTAACCAATAATTGATATACTGATCCCGAACAACCATCGAC
5697832 ATACAAAAGTTAATGCTGCCAACACCCCAACCACTCTGCATTATCAGAGAAGAAAGAACAGAGAG
66 ATACAAAAGTTAATGCTGCCAACACCCCAACCACTCTGCATTATCAGAGAAGAAAGAACAGAGAG
5697897 AAAGGTCCTAGATAGACATAGGC
131 AAAGGTCCTAGATAGACATAGGC
5697920 ATAAAAAAGT
Statistics
Matches: 152, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
154 152 1.00
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.21
Consensus pattern (154 bp):
GTACAAAACAAATTGCTTATTACTTTAACCAATAATTGATATACTGATCCCGAACAACCATCGAC
ATACAAAAGTTAATGCTGCCAACACCCCAACCACTCTGCATTATCAGAGAAGAAAGAACAGAGAG
AAAGGTCCTAGATAGACATAGGCT
Found at i:5703125 original size:29 final size:29
Alignment explanation
Indices: 5703050--5703108 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
5703040 CGCTTTCTAG
5703050 ATAGTTCAGTCTGCTTCTAACTATAAACC
1 ATAGTTCAGTCTGCTTCTAACTATAAACC
5703079 ATAGTTCAGTCTGCTTCTAACTATAAACC
1 ATAGTTCAGTCTGCTTCTAACTATAAACC
5703108 A
1 A
5703109 AGATGTCCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.32, C:0.24, G:0.10, T:0.34
Consensus pattern (29 bp):
ATAGTTCAGTCTGCTTCTAACTATAAACC
Found at i:5703658 original size:16 final size:16
Alignment explanation
Indices: 5703637--5703667 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5703627 ACAATTTTGA
5703637 AAAAAAGAAAATCTAT
1 AAAAAAGAAAATCTAT
*
5703653 AAAAAAGAAATTCTA
1 AAAAAAGAAAATCTA
5703668 GGTATCATGT
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:0.68, C:0.06, G:0.06, T:0.19
Consensus pattern (16 bp):
AAAAAAGAAAATCTAT
Found at i:5704005 original size:2 final size:2
Alignment explanation
Indices: 5703998--5704053 Score: 94
Period size: 2 Copynumber: 28.0 Consensus size: 2
5703988 TTTGATAGTA
* *
5703998 AG AG AG AG AG AG AG AG AT AG AG AG AG AG AG AG AG AG AG AA AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
5704040 AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG
5704054 GAGCCTGTTG
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.52, C:0.00, G:0.46, T:0.02
Consensus pattern (2 bp):
AG
Found at i:5714983 original size:22 final size:23
Alignment explanation
Indices: 5714955--5714999 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
5714945 ATGTAATCTT
5714955 AGATATGA-TATGCAATCTTAGA
1 AGATATGATTATGCAATCTTAGA
* *
5714977 AGATATGATTTTGTAATCTTAGA
1 AGATATGATTATGCAATCTTAGA
5715000 GATTTAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.38, C:0.07, G:0.18, T:0.38
Consensus pattern (23 bp):
AGATATGATTATGCAATCTTAGA
Found at i:5715002 original size:22 final size:21
Alignment explanation
Indices: 5714942--5715002 Score: 72
Period size: 19 Copynumber: 2.9 Consensus size: 21
5714932 AATCTTTAAG
5714942 GATATGTAATCTT--AGATAT
1 GATATGTAATCTTAGAGATAT
*
5714961 GATATGCAATCTTAGAAGATAT
1 GATATGTAATCTTAG-AGATAT
*
5714983 GATTTTGTAATCTTAGAGAT
1 GA-TATGTAATCTTAGAGAT
5715003 TTAATTTGTA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
19 12 0.34
22 12 0.34
23 11 0.31
ACGTcount: A:0.36, C:0.07, G:0.18, T:0.39
Consensus pattern (21 bp):
GATATGTAATCTTAGAGATAT
Found at i:5715607 original size:36 final size:36
Alignment explanation
Indices: 5715532--5715607 Score: 84
Period size: 36 Copynumber: 2.1 Consensus size: 36
5715522 CATACATACG
*
5715532 TTTTATAATATATACATATACGTACACATTTTTTAAT
1 TTTTATAATATATACATATACG-ACACATTTTATAAT
* *
5715569 TTTTATAA-ATATATATATAC-ACATACTTTTATATAT
1 TTTTATAATATATACATATACGACACA-TTTTATA-AT
5715605 TTT
1 TTT
5715608 CTATGTTTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
34 4 0.12
35 6 0.18
36 16 0.47
37 8 0.24
ACGTcount: A:0.38, C:0.09, G:0.01, T:0.51
Consensus pattern (36 bp):
TTTTATAATATATACATATACGACACATTTTATAAT
Found at i:5715932 original size:3 final size:3
Alignment explanation
Indices: 5715924--5715967 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
5715914 NNNNNNNNNN
5715924 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
5715968 GTTCTTGATC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:5717505 original size:18 final size:17
Alignment explanation
Indices: 5717464--5717507 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
5717454 TTTAAAATTA
*
5717464 AAAATATTTATAATTTT
1 AAAATAATTATAATTTT
**
5717481 ATTATAATTATAATTTTT
1 AAAATAATTATAA-TTTT
5717499 AAAATAATT
1 AAAATAATT
5717508 TTTTGAAATT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
AAAATAATTATAATTTT
Found at i:5732797 original size:40 final size:38
Alignment explanation
Indices: 5732689--5732820 Score: 113
Period size: 40 Copynumber: 3.4 Consensus size: 38
5732679 TTACAAGTCA
* * *
5732689 ATGAGACACGGGGTGTCAATCTATTACTTCGGATTAATTCG
1 ATGAGACACTGGGTGTCAAT-TA-TACTTCGG-TTTATCCG
* * * *
5732730 ATGAGGCACTAGGTGCCAATT-TACTTCGGTTTAGCCG
1 ATGAGACACTGGGTGTCAATTATACTTCGGTTTATCCG
**
5732767 ATGAGACACTGGGTGTCAACTTAGTACTTCGAATTATCCG
1 ATGAGACACTGGGTGTCAA-TTA-TACTTCGGTTTATCCG
**
5732807 ATGAGGTACTGGGT
1 ATGAGACACTGGGT
5732821 ACCAAACTGA
Statistics
Matches: 73, Mismatches: 15, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
37 21 0.29
38 10 0.14
40 26 0.36
41 16 0.22
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (38 bp):
ATGAGACACTGGGTGTCAATTATACTTCGGTTTATCCG
Found at i:5733024 original size:14 final size:15
Alignment explanation
Indices: 5733005--5733033 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
5732995 GAATTGAATA
5733005 TGTTATGAA-TGATT
1 TGTTATGAACTGATT
5733019 TGTTATGAACTGATT
1 TGTTATGAACTGATT
5733034 AATTGAATGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.28, C:0.03, G:0.21, T:0.48
Consensus pattern (15 bp):
TGTTATGAACTGATT
Found at i:5752989 original size:24 final size:23
Alignment explanation
Indices: 5752935--5752990 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
5752925 TTTTAATTTT
5752935 TAAATTTTTAAATATTTTTAAAA
1 TAAATTTTTAAATATTTTTAAAA
** * *
5752958 TACTTTTTTTAATTTTTTTAAAAA
1 TAAATTTTTAAATATTTTT-AAAA
5752982 TAAATTTTT
1 TAAATTTTT
5752991 GGTGCTTATT
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
23 15 0.58
24 11 0.42
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (23 bp):
TAAATTTTTAAATATTTTTAAAA
Found at i:5753806 original size:20 final size:20
Alignment explanation
Indices: 5753783--5753829 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 20
5753773 GTGGGGGTTG
*
5753783 TGGTTGCTCTGG-GGGGATTC
1 TGGTTGCTCCGGAGGGGA-TC
*
5753803 TGGTTCCTCCGGTAGGGGATC
1 TGGTTGCTCCGG-AGGGGATC
5753824 TGGTTG
1 TGGTTG
5753830 TCGGTGTTGG
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 10 0.45
21 7 0.32
22 5 0.23
ACGTcount: A:0.06, C:0.17, G:0.43, T:0.34
Consensus pattern (20 bp):
TGGTTGCTCCGGAGGGGATC
Found at i:5754090 original size:18 final size:18
Alignment explanation
Indices: 5754063--5754100 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
5754053 GAAAAATGAA
* *
5754063 ACATATAAGGGTTAGGAT
1 ACATAAAAGGGCTAGGAT
5754081 ACATAAAAGGGCTAGGAT
1 ACATAAAAGGGCTAGGAT
5754099 AC
1 AC
5754101 GCACCTGGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.42, C:0.11, G:0.26, T:0.21
Consensus pattern (18 bp):
ACATAAAAGGGCTAGGAT
Found at i:5754195 original size:30 final size:30
Alignment explanation
Indices: 5754154--5754221 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 30
5754144 ATTGAAGTGT
* * * *
5754154 TGGGCCGGGTGACTGTGTCGGTGCTGTTGC
1 TGGGCCTGGTGACTGTGGCGGCGCTGTTGA
* *
5754184 TGGGCCTGGTGATTGTGGGGGCGCTGTTGA
1 TGGGCCTGGTGACTGTGGCGGCGCTGTTGA
5754214 TGGGCCTG
1 TGGGCCTG
5754222 CGTCGTCGTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.04, C:0.18, G:0.49, T:0.29
Consensus pattern (30 bp):
TGGGCCTGGTGACTGTGGCGGCGCTGTTGA
Found at i:5755797 original size:11 final size:11
Alignment explanation
Indices: 5755783--5755841 Score: 50
Period size: 11 Copynumber: 5.4 Consensus size: 11
5755773 GAGAGCTTTA
5755783 AGAGGAATTTG
1 AGAGGAATTTG
* *
5755794 AGAGAAATATG
1 AGAGGAATTTG
5755805 AGA-GAATATTGG
1 AGAGGAAT-TT-G
* *
5755817 AGAGAAATATG
1 AGAGGAATTTG
5755828 AGA-GAATTTG
1 AGAGGAATTTG
5755838 AGAG
1 AGAG
5755842 AAATGATTTA
Statistics
Matches: 36, Mismatches: 8, Indels: 8
0.69 0.15 0.15
Matches are distributed among these distances:
10 11 0.31
11 17 0.47
12 5 0.14
13 3 0.08
ACGTcount: A:0.46, C:0.00, G:0.32, T:0.22
Consensus pattern (11 bp):
AGAGGAATTTG
Found at i:5755823 original size:23 final size:21
Alignment explanation
Indices: 5755787--5755845 Score: 100
Period size: 23 Copynumber: 2.7 Consensus size: 21
5755777 GCTTTAAGAG
5755787 GAATTTGAGAGAAATATGAGA
1 GAATTTGAGAGAAATATGAGA
5755808 GAATATTGGAGAGAAATATGAGA
1 GAAT-TT-GAGAGAAATATGAGA
5755831 GAATTTGAGAGAAAT
1 GAATTTGAGAGAAAT
5755846 GATTTAAGTG
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
21 13 0.36
22 4 0.11
23 19 0.53
ACGTcount: A:0.47, C:0.00, G:0.29, T:0.24
Consensus pattern (21 bp):
GAATTTGAGAGAAATATGAGA
Found at i:5755841 original size:10 final size:10
Alignment explanation
Indices: 5755787--5755843 Score: 60
Period size: 10 Copynumber: 5.3 Consensus size: 10
5755777 GCTTTAAGAG
5755787 GAATTTGAGA
1 GAATTTGAGA
*
5755797 GAAATATGAGA
1 G-AATTTGAGA
5755808 GAATATTGGAGA
1 GAAT-TT-GAGA
*
5755820 GAAATATGAGA
1 G-AATTTGAGA
5755831 GAATTTGAGA
1 GAATTTGAGA
5755841 GAA
1 GAA
5755844 ATGATTTAAG
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
10 15 0.38
11 15 0.38
12 6 0.15
13 3 0.08
ACGTcount: A:0.47, C:0.00, G:0.30, T:0.23
Consensus pattern (10 bp):
GAATTTGAGA
Found at i:5768780 original size:14 final size:14
Alignment explanation
Indices: 5768761--5768787 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5768751 CATCATTTGT
5768761 CTATAACCAAAACC
1 CTATAACCAAAACC
5768775 CTATAACCAAAAC
1 CTATAACCAAAAC
5768788 TCATAAACCC
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:0.52, C:0.33, G:0.00, T:0.15
Consensus pattern (14 bp):
CTATAACCAAAACC
Found at i:5773971 original size:26 final size:27
Alignment explanation
Indices: 5773922--5773976 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
5773912 AAAATATTTT
5773922 TATTTTTATTTCTAATTTGTAAAAAAA
1 TATTTTTATTTCTAATTTGTAAAAAAA
*
5773949 TATTTTTATTT-T-ATTTTTAAAAAGAA
1 TATTTTTATTTCTAATTTGTAAAAA-AA
5773975 TA
1 TA
5773977 CAAAAAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 10 0.38
26 5 0.19
27 11 0.42
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.55
Consensus pattern (27 bp):
TATTTTTATTTCTAATTTGTAAAAAAA
Found at i:5780172 original size:25 final size:25
Alignment explanation
Indices: 5780144--5780191 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
5780134 TTGCATAATT
*
5780144 ATGTCATGATT-CTATCACTACAATC
1 ATGTCA-GATTACTATCACAACAATC
5780169 ATGTCAGATTACTATCACAACAA
1 ATGTCAGATTACTATCACAACAA
5780192 CCTTCATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.38, C:0.23, G:0.08, T:0.31
Consensus pattern (25 bp):
ATGTCAGATTACTATCACAACAATC
Found at i:5789191 original size:2 final size:2
Alignment explanation
Indices: 5789184--5789222 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
5789174 TAAGTGCAAT
5789184 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5789223 CCGCCACTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5789307 original size:24 final size:24
Alignment explanation
Indices: 5789251--5789308 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
5789241 ACCAATTTGT
5789251 ATAAAAT-AAAAAAAAATCGTAAA
1 ATAAAATGAAAAAAAAATCGTAAA
** *
5789274 CGAAATTGAAAAAAAAAT-GTAAA
1 ATAAAATGAAAAAAAAATCGTAAA
5789297 ATAAACATGAAA
1 ATAAA-ATGAAA
5789309 GGGTTACTAA
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
23 12 0.44
24 15 0.56
ACGTcount: A:0.69, C:0.05, G:0.09, T:0.17
Consensus pattern (24 bp):
ATAAAATGAAAAAAAAATCGTAAA
Found at i:5795786 original size:165 final size:169
Alignment explanation
Indices: 5795528--5795835 Score: 464
Period size: 168 Copynumber: 1.8 Consensus size: 169
5795518 CAAGAATTTC
* * *
5795528 TTCATTTCCATGCATTTCTCATCTTCACCACTTTCCTTCCTTTTTTCTTCTCGTTTTCTCCATTT
1 TTCATTTCCATGCA-TTCTCATCTTCACCACTTTCCTTCCTTTTATCTTCTCATTTTCTCCACTT
*
5795593 TCATCTACTATTTTATTGATTATAAATTG-G-ACATATTCTTTAAAATCTCTACTTCA-CATTCT
65 TCATCTACTATTTTATTGATTATAAATTGAGAACATATTCTCTAAAATCTCTACTTCATC-TTCT
5795655 CTCTTTAATATCTCATTTGTCGAGAATTTCTTCATTTCTTT
129 CTCTTTAATATCTCATTTGTCGAGAATTTCTTCATTTCTTT
* *
5795696 TTCATTTCCATGCA-TCTCATCTTCACCACTTTTCTTCC-TTTATCTTCTCATTTTCTCTACTTT
1 TTCATTTCCATGCATTCTCATCTTCACCACTTTCCTTCCTTTTATCTTCTCATTTTCTCCACTTT
* * * *
5795759 CATCTACTATTTTCTTGCTTCTAAATTGATGAACATATTCTCTAGAATCTCTACTTCATCTTCTC
66 CATCTACTATTTTATTGATTATAAATTGA-GAACATATTCTCTAAAATCTCTACTTCATCTTCTC
5795824 TCTTTAATATCT
130 TCTTTAATATCT
5795836 AAGGAAATTT
Statistics
Matches: 126, Mismatches: 10, Indels: 8
0.88 0.07 0.06
Matches are distributed among these distances:
165 46 0.37
166 23 0.18
167 1 0.01
168 55 0.44
169 1 0.01
ACGTcount: A:0.20, C:0.25, G:0.04, T:0.50
Consensus pattern (169 bp):
TTCATTTCCATGCATTCTCATCTTCACCACTTTCCTTCCTTTTATCTTCTCATTTTCTCCACTTT
CATCTACTATTTTATTGATTATAAATTGAGAACATATTCTCTAAAATCTCTACTTCATCTTCTCT
CTTTAATATCTCATTTGTCGAGAATTTCTTCATTTCTTT
Found at i:5795993 original size:13 final size:11
Alignment explanation
Indices: 5795961--5796003 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
5795951 TTCATCCTTC
*
5795961 AATAAAATAAT
1 AATAAAATATT
5795972 AAT-AAATATCT
1 AATAAAATAT-T
5795983 AAGTAAAATATT
1 AA-TAAAATATT
5795995 AATAAAATA
1 AATAAAATA
5796004 ATATTTAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 5 0.18
11 13 0.46
12 4 0.14
13 6 0.21
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (11 bp):
AATAAAATATT
Found at i:5811083 original size:30 final size:30
Alignment explanation
Indices: 5811047--5811110 Score: 128
Period size: 30 Copynumber: 2.1 Consensus size: 30
5811037 CTCGTTTAAA
5811047 GTTTGAGTTAGCCAACTTTTTTTCCTTTCT
1 GTTTGAGTTAGCCAACTTTTTTTCCTTTCT
5811077 GTTTGAGTTAGCCAACTTTTTTTCCTTTCT
1 GTTTGAGTTAGCCAACTTTTTTTCCTTTCT
5811107 GTTT
1 GTTT
5811111 TTTTTTTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.12, C:0.19, G:0.14, T:0.55
Consensus pattern (30 bp):
GTTTGAGTTAGCCAACTTTTTTTCCTTTCT
Found at i:5813929 original size:26 final size:26
Alignment explanation
Indices: 5813899--5813948 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
5813889 ACAACGAGAA
*
5813899 TGTCAACTAAACTAGTAGGGGTGATT
1 TGTCAACTAAACTAGTAGAGGTGATT
*
5813925 TGTCAACTAAATTAGTAGAGGTGA
1 TGTCAACTAAACTAGTAGAGGTGA
5813949 GTATAGTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.34, C:0.10, G:0.26, T:0.30
Consensus pattern (26 bp):
TGTCAACTAAACTAGTAGAGGTGATT
Found at i:5828508 original size:19 final size:20
Alignment explanation
Indices: 5828470--5828531 Score: 65
Period size: 19 Copynumber: 3.0 Consensus size: 20
5828460 CATGTTAATT
5828470 TTTTTAAAATTTAAATTTTTAGT-
1 TTTTTAAAA-TT--ATTTTTA-TA
5828493 TTTTTAAAA-TATTTTTATA
1 TTTTTAAAATTATTTTTATA
5828512 TTTTTAAAATTATTTGTTAT
1 TTTTTAAAATTATTT-TTAT
5828532 CATGACATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
18 1 0.03
19 16 0.44
20 5 0.14
21 5 0.14
23 9 0.25
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTTAAAATTATTTTTATA
Found at i:5835660 original size:71 final size:71
Alignment explanation
Indices: 5835543--5835710 Score: 300
Period size: 71 Copynumber: 2.4 Consensus size: 71
5835533 TAGGTTAATA
5835543 TAAAAGCAGATTCCTCCTTATCTGCTAATGTCCTTTATGAAGGAGTCATGTCCTTTATGTCTGTA
1 TAAAAGCAGATTCCTCCTTATCTGCTAATGTCCTTTATGAAGGAGTCATGTCCTTTATGTCTGTA
5835608 AAAATG
66 AAAATG
* * * *
5835614 TAAAAGCAGATTCTTTCTTATCTGCTAATGTCCTTTATGAATGAGTCATGTCCTTTGTGTCTGTA
1 TAAAAGCAGATTCCTCCTTATCTGCTAATGTCCTTTATGAAGGAGTCATGTCCTTTATGTCTGTA
5835679 AAAATG
66 AAAATG
5835685 TAAAAGCAGATTCCTCCTTATCTGCT
1 TAAAAGCAGATTCCTCCTTATCTGCT
5835711 TATCCTCCTC
Statistics
Matches: 91, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
71 91 1.00
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.38
Consensus pattern (71 bp):
TAAAAGCAGATTCCTCCTTATCTGCTAATGTCCTTTATGAAGGAGTCATGTCCTTTATGTCTGTA
AAAATG
Found at i:5843068 original size:19 final size:19
Alignment explanation
Indices: 5843027--5843068 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
5843017 TCAAAATTTT
* *
5843027 TATTTTTATTTTTAAATTG
1 TATTTTTATTTATAAATTA
5843046 TATTTTTATTTAATAAA-TA
1 TATTTTTATTT-ATAAATTA
5843065 TATT
1 TATT
5843069 ATTTTCATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
TATTTTTATTTATAAATTA
Found at i:5850390 original size:17 final size:18
Alignment explanation
Indices: 5850368--5850401 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
5850358 AATCCATACA
5850368 AACTCAATCATT-TCATC
1 AACTCAATCATTATCATC
*
5850385 AACTCATTCATTATCAT
1 AACTCAATCATTATCAT
5850402 TTCTATTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.35, C:0.26, G:0.00, T:0.38
Consensus pattern (18 bp):
AACTCAATCATTATCATC
Found at i:5853044 original size:51 final size:51
Alignment explanation
Indices: 5852963--5853163 Score: 377
Period size: 51 Copynumber: 3.9 Consensus size: 51
5852953 ACTTCTGATC
*
5852963 AGTGACAAGTGATAAGT-AGTAGCTTCAGCTACACTTATCTGATCAGTGACA
1 AGTGGCAAGTGATAAGTGA-TAGCTTCAGCTACACTTATCTGATCAGTGACA
5853014 AGTGGCAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAGTGACA
1 AGTGGCAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAGTGACA
5853065 AGTGGCAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAGTGACA
1 AGTGGCAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAGTGACA
5853116 AGTGGCAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAGTG
1 AGTGGCAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAGTG
5853164 GCTACACTTA
Statistics
Matches: 148, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
51 147 0.99
52 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.28
Consensus pattern (51 bp):
AGTGGCAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAGTGACA
Found at i:5853125 original size:102 final size:103
Alignment explanation
Indices: 5852963--5853290 Score: 397
Period size: 102 Copynumber: 3.1 Consensus size: 103
5852953 ACTTCTGATC
5852963 AGTGACAAGTGATAAGT-AGTAGCTTCAGCTACACTTATCTGATCAGTGACAAGTGGCAAGTGAT
1 AGTGACAAGTGATAAGTGA-TAGCTTCAGCTACACTTATCTGATCAGTGACAAGTGGCAAGTGAT
5853027 AAGTGATAGCTTCAGCTACACTTATCTGATCAGTG-ACA
65 AAGTGATAGCTTCAGCTACACTTATCTGATCAGTGTACA
*
5853065 AGTGGCAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAGTGACAAGTGGCAAGTGATA
1 AGTGACAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAGTGACAAGTGGCAAGTGATA
5853130 AGTGATAGCTTCAGCTACACTTATCTGATCAGTGGCTACACTTATCTGA
66 AGTGATAGCTTCAGCTACACTTATCTGATCAGT-G-------TA-C--A
* * *
5853179 TCAGTGACAAGTGATGAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGT---AA-TG-
1 --AGTGACAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAGTGACAAGTGGCAAGTGA
* * *
5853239 --AGTGGTAGCTTTAGCTACACTTATATGATCAG-GTACA
64 TAAGTGATAGCTTCAGCTACACTTATCTGATCAGTGTACA
5853276 AGTGACAAGTGATAA
1 AGTGACAAGTGATAA
5853291 ATGTGATCCG
Statistics
Matches: 202, Mismatches: 9, Indels: 37
0.81 0.04 0.15
Matches are distributed among these distances:
95 14 0.07
97 1 0.00
99 1 0.00
100 2 0.01
102 95 0.47
103 2 0.01
107 1 0.00
109 29 0.14
111 1 0.00
112 3 0.01
113 2 0.01
114 1 0.00
116 50 0.25
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (103 bp):
AGTGACAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAGTGACAAGTGGCAAGTGATA
AGTGATAGCTTCAGCTACACTTATCTGATCAGTGTACA
Found at i:5853167 original size:21 final size:21
Alignment explanation
Indices: 5853143--5853184 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
5853133 GATAGCTTCA
5853143 GCTACACTTATCTGATCAGTG
1 GCTACACTTATCTGATCAGTG
5853164 GCTACACTTATCTGATCAGTG
1 GCTACACTTATCTGATCAGTG
5853185 ACAAGTGATG
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:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (21 bp):
GCTACACTTATCTGATCAGTG
Found at i:5853227 original size:44 final size:44
Alignment explanation
Indices: 5853164--5853280 Score: 200
Period size: 44 Copynumber: 2.7 Consensus size: 44
5853154 CTGATCAGTG
5853164 GCTACACTTATCTGATCAGTGACAAGTGATGAGTGGTAGCTTTA
1 GCTACACTTATCTGATCAGTGACAAGTGATGAGTGGTAGCTTTA
*
5853208 GCTACACTTATCTGATCAGTGACAAGTAATGAGTGGTAGCTTTA
1 GCTACACTTATCTGATCAGTGACAAGTGATGAGTGGTAGCTTTA
*
5853252 GCTACACTTATATGATCAG-GTACAAGTGA
1 GCTACACTTATCTGATCAGTG-ACAAGTGA
5853281 CAAGTGATAA
Statistics
Matches: 69, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
43 1 0.01
44 68 0.99
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (44 bp):
GCTACACTTATCTGATCAGTGACAAGTGATGAGTGGTAGCTTTA
Found at i:5866037 original size:22 final size:22
Alignment explanation
Indices: 5866012--5866055 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
5866002 CATATAAAAT
*
5866012 TATAATAAATCTTTAATAGTAA
1 TATAATAAATCTTTAACAGTAA
*
5866034 TATAATAAGTCTTTAACAGTAA
1 TATAATAAATCTTTAACAGTAA
5866056 ACACAGAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.39
Consensus pattern (22 bp):
TATAATAAATCTTTAACAGTAA
Found at i:5868787 original size:3 final size:3
Alignment explanation
Indices: 5868779--5868809 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
5868769 TCTCGAGGTC
*
5868779 CAT CAT CAT CAT CAT CAT CAT CAT CAC CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
5868810 CTGTAGGGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.32, C:0.39, G:0.00, T:0.29
Consensus pattern (3 bp):
CAT
Found at i:5869786 original size:2 final size:2
Alignment explanation
Indices: 5869779--5869803 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5869769 CTGTAAAAGA
5869779 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
5869804 ATTAAGTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5873899 original size:318 final size:317
Alignment explanation
Indices: 5873323--5873957 Score: 1225
Period size: 318 Copynumber: 2.0 Consensus size: 317
5873313 CAAGAAAAAT
5873323 CTTCCACTTTCTCAATTGGATAAAGAGATTCAAAGTTTTTCATATTGAAAAAATAAACTATGCTT
1 CTTCCACTTTCTCAATTGGATAAAGAGATTCAAAGTTTTTCATATTGAAAAAATAAACTATGCTT
* *
5873388 CATTTAACCAGTGCCAATGGTCAAATCAAATCCTTTTCTGAATCACTCTGGATGTAAAACATGAA
66 CATTTAACCAGTGCCAATGGTCAAACCAAATCCTTTTCTGAATCACTCGGGATGTAAAACATGAA
*
5873453 GGCAAAACATTTCGATCAAGGTCAGAATGATTAAAGATGCAAAAGCAACATACAACAGTTTACGA
131 GGCAAAACATTTCGATCAAGGTCAGAATGATTAAAGATGCAAAAGCAACATACAACAGTTAACGA
5873518 CAAAATTAGCAAAATAGCCATTAATTTACTCATTGAGTAGAATCCAGAACCAAATATGCAGATAC
196 CAAAATTAGCAAAATAGCCATTAATTTACTCATTGAGTAGAATCCAGAACCAAATATGCAGATAC
5873583 TGGGAGAGAAAAGAAAATCCTAAAGCTAAAATTAAATTTATGCAAATTTCATCTGGG
261 TGGGAGAGAAAAGAAAATCCTAAAGCTAAAATTAAATTTATGCAAATTTCATCTGGG
5873640 CTTCCACTTTCTCAATTGGATAAAGAGATTCAAAGTTTTTCATATTGAAAAAATAAACTATGCTT
1 CTTCCACTTTCTCAATTGGATAAAGAGATTCAAAGTTTTTCATATTGAAAAAATAAACTATGCTT
*
5873705 CATTTAACCAGTGCCAATGGTCAAACCAAATCCTCTTTCTGAATCATTCGGGATGTAAAACATGA
66 CATTTAACCAGTGCCAATGGTCAAACCAAATCCT-TTTCTGAATCACTCGGGATGTAAAACATGA
5873770 AGGCAAAACATTTCGATCAAGGTCAGAATGATTAAAGATGCAAAAGCAACATACAACAGTTAACG
130 AGGCAAAACATTTCGATCAAGGTCAGAATGATTAAAGATGCAAAAGCAACATACAACAGTTAACG
5873835 ACAAAATTAGCAAAATAGCCATTAATTTACTCATTGAGTAGAATCCAGAACCAAATATGCAGATA
195 ACAAAATTAGCAAAATAGCCATTAATTTACTCATTGAGTAGAATCCAGAACCAAATATGCAGATA
5873900 CTGGGAGAGAAAAGAAAATCCTAAAGCTAAAATTAAATTTATGCAAATTTCATCTGGG
260 CTGGGAGAGAAAAGAAAATCCTAAAGCTAAAATTAAATTTATGCAAATTTCATCTGGG
5873958 TTCTAGCAGG
Statistics
Matches: 313, Mismatches: 4, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
317 98 0.31
318 215 0.69
ACGTcount: A:0.41, C:0.17, G:0.15, T:0.27
Consensus pattern (317 bp):
CTTCCACTTTCTCAATTGGATAAAGAGATTCAAAGTTTTTCATATTGAAAAAATAAACTATGCTT
CATTTAACCAGTGCCAATGGTCAAACCAAATCCTTTTCTGAATCACTCGGGATGTAAAACATGAA
GGCAAAACATTTCGATCAAGGTCAGAATGATTAAAGATGCAAAAGCAACATACAACAGTTAACGA
CAAAATTAGCAAAATAGCCATTAATTTACTCATTGAGTAGAATCCAGAACCAAATATGCAGATAC
TGGGAGAGAAAAGAAAATCCTAAAGCTAAAATTAAATTTATGCAAATTTCATCTGGG
Found at i:5886919 original size:2 final size:2
Alignment explanation
Indices: 5886912--5886936 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5886902 TTTAAGGTAT
5886912 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 T
5886937 GAGGTAGAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5889136 original size:21 final size:21
Alignment explanation
Indices: 5889110--5889151 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
5889100 CCGAGTCATA
*
5889110 TCGATAAGTTGGAGGTTAAAC
1 TCGATAAGTTAGAGGTTAAAC
5889131 TCGATAAGTTAGAGGTTAAAC
1 TCGATAAGTTAGAGGTTAAAC
5889152 ATTGAATAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.10, G:0.26, T:0.29
Consensus pattern (21 bp):
TCGATAAGTTAGAGGTTAAAC
Found at i:5897455 original size:87 final size:87
Alignment explanation
Indices: 5897313--5897478 Score: 323
Period size: 87 Copynumber: 1.9 Consensus size: 87
5897303 GAAAACAACT
5897313 ACTAAATTTGGGATAGGTTTGTTTGTGATAATAGTAGTAGGATCAGGAGGTATAATGAGGAGAGT
1 ACTAAATTTGGGATAGGTTTGTTTGTGATAATAGTAGTAGGATCAGGAGGTATAATGAGGAGAGT
5897378 ATTAAGGGTCTCATGAATAACA
66 ATTAAGGGTCTCATGAATAACA
*
5897400 ACTAAATTTGGGATAGGTTTGTTTGTGATAGTAGTAGTAGGATCAGGAGGTATAATGAGGAGAGT
1 ACTAAATTTGGGATAGGTTTGTTTGTGATAATAGTAGTAGGATCAGGAGGTATAATGAGGAGAGT
5897465 ATTAAGGGTCTCAT
66 ATTAAGGGTCTCAT
5897479 CTTCATTAAA
Statistics
Matches: 78, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
87 78 1.00
ACGTcount: A:0.33, C:0.05, G:0.30, T:0.32
Consensus pattern (87 bp):
ACTAAATTTGGGATAGGTTTGTTTGTGATAATAGTAGTAGGATCAGGAGGTATAATGAGGAGAGT
ATTAAGGGTCTCATGAATAACA
Found at i:5944740 original size:20 final size:20
Alignment explanation
Indices: 5944715--5944752 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5944705 CATAAAATGA
*
5944715 TTTCTGGAAAATGTTTTATT
1 TTTCTGGAAAATGATTTATT
*
5944735 TTTCTGTAAAATGATTTA
1 TTTCTGGAAAATGATTTA
5944753 CTGGAAAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.05, G:0.13, T:0.53
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTATT
Found at i:5948399 original size:20 final size:20
Alignment explanation
Indices: 5948365--5948406 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
5948355 AACTATTTAA
** *
5948365 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
5948385 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
5948405 AT
1 AT
5948407 GTGTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:5953357 original size:20 final size:20
Alignment explanation
Indices: 5953323--5953364 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
5953313 AACTGTTTAA
** *
5953323 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
5953343 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
5953363 AT
1 AT
5953365 GTGTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:5956471 original size:50 final size:50
Alignment explanation
Indices: 5956356--5956646 Score: 411
Period size: 50 Copynumber: 5.8 Consensus size: 50
5956346 GATCATAACA
* * ** *
5956356 TGCCAAAGCCATGTCCCAGACATAGTCTTACATGGGATGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* **
5956407 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
5956457 TGCCAACGCCATGTCCCAGACATGGTCTTATATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * * *
5956507 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTATCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
5956557 TGCCAATGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * *
5956607 TGCCAATTCCATGTCCCAGACATGGTCTTATATGAGACCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCT
5956647 ATTTACCCAA
Statistics
Matches: 214, Mismatches: 26, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
50 182 0.85
51 32 0.15
ACGTcount: A:0.21, C:0.30, G:0.22, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:5957008 original size:30 final size:30
Alignment explanation
Indices: 5956973--5957029 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
5956963 CATCGACTCT
*
5956973 AACTTTTTCAAAATTACAATTTTGCCCATA
1 AACTTTTGCAAAATTACAATTTTGCCCATA
* *
5957003 AACTTTTGCATAATTACATTTTTGCCC
1 AACTTTTGCAAAATTACAATTTTGCCC
5957030 CAAGGCTTGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.32, C:0.21, G:0.05, T:0.42
Consensus pattern (30 bp):
AACTTTTGCAAAATTACAATTTTGCCCATA
Found at i:5958121 original size:75 final size:78
Alignment explanation
Indices: 5958010--5958216 Score: 201
Period size: 80 Copynumber: 2.7 Consensus size: 78
5958000 ATTTACATGT
* * * * *
5958010 ATATGTTTTTGTATTGAGTTTGGGTATAATTTTTATATAAGTTTATATGA-AGTTCGAA-A-ATA
1 ATATGTTTTTGTATTGAATTTAGGTATGA-TATTATATAAGTTTATATGAGA-CTCGAATATATA
5958072 CAAA--TATA-ATTGA
64 CAAACTTATATA-TGA
* * * *
5958085 ATATGTTTTTGTGTTAAATTTAGGTATGACTATTATATAAAGTATGTATGAGACTCGAATATATA
1 ATATGTTTTTGTATTGAATTTAGGTATGA-TATTATAT-AAGTTTATATGAGACTCGAATATATA
*
5958150 CAAACTTATATATGT
64 CAAACTTATATATGA
* * *
5958165 ACATGTTTATGTATTGAATTTAGGTATGATAATTATATAAGTTTATGTGAGA
1 ATATGTTTTTGTATTGAATTTAGGTATGAT-ATTATATAAGTTTATATGAGA
5958217 TTCAATTATG
Statistics
Matches: 106, Mismatches: 18, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
75 31 0.29
76 15 0.14
77 2 0.02
78 7 0.07
79 12 0.11
80 38 0.36
81 1 0.01
ACGTcount: A:0.36, C:0.04, G:0.16, T:0.44
Consensus pattern (78 bp):
ATATGTTTTTGTATTGAATTTAGGTATGATATTATATAAGTTTATATGAGACTCGAATATATACA
AACTTATATATGA
Found at i:5960359 original size:2 final size:2
Alignment explanation
Indices: 5960352--5960381 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5960342 TACCCTCGAT
5960352 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5960382 AAGAAGACCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5961544 original size:11 final size:11
Alignment explanation
Indices: 5961527--5961556 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
5961517 AGGTTTGACT
5961527 TTGTTGATTGA
1 TTGTTGATTGA
*
5961538 TTTTTGATTGA
1 TTGTTGATTGA
5961549 TTGTTGAT
1 TTGTTGAT
5961557 AGATCATAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.17, C:0.00, G:0.23, T:0.60
Consensus pattern (11 bp):
TTGTTGATTGA
Found at i:5965595 original size:22 final size:22
Alignment explanation
Indices: 5965564--5965649 Score: 118
Period size: 22 Copynumber: 3.9 Consensus size: 22
5965554 TTGGTGGATT
* * *
5965564 TAACGAACTAAACCCTCATGGC
1 TAACGTACTAAGCTCTCATGGC
5965586 TAACGTACTAAGCTCTCATGGC
1 TAACGTACTAAGCTCTCATGGC
**
5965608 TAACGTACTAAGCTCTCATGTT
1 TAACGTACTAAGCTCTCATGGC
*
5965630 TCACGTACTAAGCTCTCATG
1 TAACGTACTAAGCTCTCATG
5965650 TTTGAACAAT
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 58 1.00
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (22 bp):
TAACGTACTAAGCTCTCATGGC
Found at i:5973002 original size:31 final size:31
Alignment explanation
Indices: 5972967--5973029 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
5972957 TATAATTTTA
*
5972967 TTATTAAATTATTTAAAAGTTTTTATTTAAG
1 TTATTAAATTATTCAAAAGTTTTTATTTAAG
*
5972998 TTATTGAATTATTCAAAAGTTTTTATTTAAG
1 TTATTAAATTATTCAAAAGTTTTTATTTAAG
5973029 T
1 T
5973030 GACTGATTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.37, C:0.02, G:0.08, T:0.54
Consensus pattern (31 bp):
TTATTAAATTATTCAAAAGTTTTTATTTAAG
Found at i:5973044 original size:27 final size:29
Alignment explanation
Indices: 5972973--5973048 Score: 84
Period size: 31 Copynumber: 2.6 Consensus size: 29
5972963 TTTATTATTA
* *
5972973 AATTATTTAAAAGTTTTTATTTAAGTTATTG
1 AATTA-TT-AAAGTTTTTATTTAAGTGACTG
5973004 AATTATTCAAAAGTTTTTATTTAAGTGACTG
1 AATTATT--AAAGTTTTTATTTAAGTGACTG
5973035 -ATTATT-AAGTTTTT
1 AATTATTAAAGTTTTT
5973049 TTTTTATTTC
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
27 8 0.19
30 8 0.19
31 26 0.62
ACGTcount: A:0.34, C:0.03, G:0.11, T:0.53
Consensus pattern (29 bp):
AATTATTAAAGTTTTTATTTAAGTGACTG
Found at i:5974007 original size:3 final size:3
Alignment explanation
Indices: 5973999--5974033 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
5973989 GCCTTCCCAG
5973999 ATA ATA ATA ATA ATA ATA ATA AT- ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
5974034 TATTGTTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:5976672 original size:3 final size:3
Alignment explanation
Indices: 5976666--5976703 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
5976656 CTACTACTAC
5976666 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
5976704 ACAACTAGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:5988467 original size:19 final size:19
Alignment explanation
Indices: 5988443--5988481 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
5988433 ACGGTGTAAG
5988443 TTAGCTTTTCGTAATGTGC
1 TTAGCTTTTCGTAATGTGC
5988462 TTAGCTTTTCGTAATGTGC
1 TTAGCTTTTCGTAATGTGC
5988481 T
1 T
5988482 GAAAGTTGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.21, T:0.49
Consensus pattern (19 bp):
TTAGCTTTTCGTAATGTGC
Found at i:5992335 original size:124 final size:124
Alignment explanation
Indices: 5992115--5992359 Score: 463
Period size: 124 Copynumber: 2.0 Consensus size: 124
5992105 TAATCAGCAC
*
5992115 AAGGAATAGACAACAACAACAGCAACAATAGTAAAATTTAATTAATCTGATAATGTTCTATTTAA
1 AAGGAATAGACAACAACAACAGCAACAATAATAAAATTTAATTAATCTGATAATGTTCTATTTAA
*
5992180 AGTTAACCTAATAAGGAAGCCTTTCCAGATGTGAGAAAAACATTATCTACTAACCTAAT
66 AGTTAACCTAACAAGGAAGCCTTTCCAGATGTGAGAAAAACATTATCTACTAACCTAAT
*
5992239 AAGGAATAGACAACAACAACAGCAACAATAATCAAATTTAATTAATCTGATAATGTTCTATTTAA
1 AAGGAATAGACAACAACAACAGCAACAATAATAAAATTTAATTAATCTGATAATGTTCTATTTAA
5992304 AGTTAACCTAACAAGGAAGCCTTTCCAGATGTGAGAAAAACATTATCTACTAACCT
66 AGTTAACCTAACAAGGAAGCCTTTCCAGATGTGAGAAAAACATTATCTACTAACCT
5992360 CCAAAAGCCT
Statistics
Matches: 118, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
124 118 1.00
ACGTcount: A:0.45, C:0.16, G:0.12, T:0.27
Consensus pattern (124 bp):
AAGGAATAGACAACAACAACAGCAACAATAATAAAATTTAATTAATCTGATAATGTTCTATTTAA
AGTTAACCTAACAAGGAAGCCTTTCCAGATGTGAGAAAAACATTATCTACTAACCTAAT
Found at i:6006887 original size:19 final size:19
Alignment explanation
Indices: 6006838--6006889 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
6006828 ATAATACTAT
6006838 TTAAAATTAAAA-TTAATTA
1 TTAAAA-TAAAATTTAATTA
*
6006857 -TAAATATCAAAATTTATTTA
1 TTAAA-AT-AAAATTTAATTA
6006877 TTAAAATAAAATT
1 TTAAAATAAAATT
6006890 GTAGTATTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
18 5 0.18
19 11 0.39
20 8 0.29
21 4 0.14
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (19 bp):
TTAAAATAAAATTTAATTA
Found at i:6014043 original size:3 final size:3
Alignment explanation
Indices: 6014035--6014076 Score: 66
Period size: 3 Copynumber: 13.7 Consensus size: 3
6014025 TTCGTTTTAG
*
6014035 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAAT TTT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TA
6014077 ACCTCGATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 33 0.92
4 3 0.08
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:6017602 original size:26 final size:28
Alignment explanation
Indices: 6017554--6017612 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 28
6017544 TTTCAAATAG
** *
6017554 ATGAACTAATTTTTTTTTTAATA-TTAA
1 ATGAACTAATTTTTTTTAAAATACATAA
*
6017581 ATGAACT-GTTTTTTTTAAAATACATAA
1 ATGAACTAATTTTTTTTAAAATACATAA
6017608 ATGAA
1 ATGAA
6017613 AAACAAGAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 12 0.44
27 15 0.56
ACGTcount: A:0.41, C:0.05, G:0.07, T:0.47
Consensus pattern (28 bp):
ATGAACTAATTTTTTTTAAAATACATAA
Found at i:6023718 original size:17 final size:18
Alignment explanation
Indices: 6023696--6023731 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
6023686 TGATAGAGTG
*
6023696 TGTATAATAA-ACTAAAA
1 TGTATAAAAATACTAAAA
6023713 TGTATAAAAATACTAAAA
1 TGTATAAAAATACTAAAA
6023731 T
1 T
6023732 AAAGCTTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.31
Consensus pattern (18 bp):
TGTATAAAAATACTAAAA
Found at i:6027060 original size:25 final size:25
Alignment explanation
Indices: 6027032--6027099 Score: 66
Period size: 26 Copynumber: 2.7 Consensus size: 25
6027022 CCGGATAGCT
*
6027032 ATATATCAGGAAGTTCA-AGCGAGCC
1 ATATATCAGGAAGCTCACAG-GAGCC
* *
6027057 ATATAACAGGGAGCTCACGAGGAGCC
1 ATATATCAGGAAGCTCAC-AGGAGCC
* *
6027083 ATATATCGGGACGCTCA
1 ATATATCAGGAAGCTCA
6027100 TAAAGAGCTG
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
25 14 0.41
26 18 0.53
27 2 0.06
ACGTcount: A:0.34, C:0.22, G:0.26, T:0.18
Consensus pattern (25 bp):
ATATATCAGGAAGCTCACAGGAGCC
Found at i:6027107 original size:26 final size:26
Alignment explanation
Indices: 6027052--6027107 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 26
6027042 AAGTTCAAGC
* *
6027052 GAGCCATATAACAGGGAGCTCACGAG
1 GAGCCATATAACAGGGAGCTCACAAA
* *
6027078 GAGCCATATATC-GGGACGCTCATAAA
1 GAGCCATATAACAGGGA-GCTCACAAA
6027104 GAGC
1 GAGC
6027108 TGCGGTATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
25 4 0.16
26 21 0.84
ACGTcount: A:0.34, C:0.23, G:0.29, T:0.14
Consensus pattern (26 bp):
GAGCCATATAACAGGGAGCTCACAAA
Found at i:6037603 original size:22 final size:22
Alignment explanation
Indices: 6037565--6037618 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
6037555 CCGGCCTATT
* * *
6037565 TTTTAATAAATACAAAAAAATTG
1 TTTTAA-AAATTCAAAAAAAGTA
6037588 TTTTAAAAATT-AAAAAAAGTA
1 TTTTAAAAATTCAAAAAAAGTA
6037609 TTTTAAAAAT
1 TTTTAAAAAT
6037619 ATTTTAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 18 0.64
22 4 0.14
23 6 0.21
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.37
Consensus pattern (22 bp):
TTTTAAAAATTCAAAAAAAGTA
Found at i:6037643 original size:39 final size:39
Alignment explanation
Indices: 6037592--6037674 Score: 139
Period size: 39 Copynumber: 2.1 Consensus size: 39
6037582 AAATTGTTTT
* *
6037592 AAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTA
1 AAAAATTAAAAAAAATATTTTAAAAATATTTTAAAAATA
*
6037631 AAAAATTTAAAAAAATATTTTAAAAATATTTTAAAAATA
1 AAAAATTAAAAAAAATATTTTAAAAATATTTTAAAAATA
6037670 AAAAA
1 AAAAA
6037675 GTATTTTAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (39 bp):
AAAAATTAAAAAAAATATTTTAAAAATATTTTAAAAATA
Found at i:6037685 original size:11 final size:11
Alignment explanation
Indices: 6037601--6037669 Score: 69
Period size: 11 Copynumber: 6.6 Consensus size: 11
6037591 TAAAAATTAA
6037601 AAAAAGTATTTT
1 AAAAA-TATTTT
6037613 AAAAATATTTT
1 AAAAATATTTT
6037624 --AAA-A--TT
1 AAAAATATTTT
*
6037630 AAAAA-ATTTAA
1 AAAAATATTT-T
6037641 AAAAATATTTT
1 AAAAATATTTT
6037652 AAAAATATTTT
1 AAAAATATTTT
6037663 AAAAATA
1 AAAAATA
6037670 AAAAAGTATT
Statistics
Matches: 49, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
6 2 0.04
8 5 0.10
9 3 0.06
10 1 0.02
11 29 0.59
12 9 0.18
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:6039273 original size:2 final size:2
Alignment explanation
Indices: 6039266--6039299 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
6039256 TCATCTTGTA
6039266 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
6039300 TAATTCGTAA
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:6056388 original size:20 final size:20
Alignment explanation
Indices: 6056363--6056428 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
6056353 TAACAAAAAA
*
6056363 TCAAAATAATTTTCAAAATT
1 TCAAAATAATTTTAAAAATT
* *
6056383 TGAAAATAATTTTTAAAA-T
1 TCAAAATAATTTTAAAAATT
6056402 TCAAAAT-ATTTATAAAAATT
1 TCAAAATAATTT-TAAAAATT
*
6056422 TTAAAAT
1 TCAAAAT
6056429 TATAAATTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
18 4 0.10
19 12 0.31
20 23 0.59
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.41
Consensus pattern (20 bp):
TCAAAATAATTTTAAAAATT
Found at i:6056419 original size:19 final size:19
Alignment explanation
Indices: 6056357--6056421 Score: 69
Period size: 19 Copynumber: 3.4 Consensus size: 19
6056347 CTCTCTTAAC
*
6056357 AAAAAATCAAAATAATTTT
1 AAAAATTCAAAATAATTTT
* *
6056376 CAAAATTTGAAAATAATTTT
1 -AAAAATTCAAAATAATTTT
*
6056396 TAAAATTCAAAAT-ATTTAT
1 AAAAATTCAAAATAATTT-T
6056415 AAAAATT
1 AAAAATT
6056422 TTAAAATTAT
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
18 4 0.11
19 17 0.46
20 16 0.43
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.37
Consensus pattern (19 bp):
AAAAATTCAAAATAATTTT
Found at i:6056440 original size:27 final size:26
Alignment explanation
Indices: 6056374--6056446 Score: 78
Period size: 27 Copynumber: 2.7 Consensus size: 26
6056364 CAAAATAATT
*
6056374 TTCAAAAT-TTGAAAATAATTTTTAAAA
1 TTCAAAATATTTAAAA-AA-TTTTAAAA
6056401 TTCAAAATATTTATAAAAATTTTAAAA
1 TTCAAAATATTTA-AAAAATTTTAAAA
*
6056428 TT-ATAAATTTTTAAAAAAT
1 TTCA-AAATATTTAAAAAAT
6056447 ATATCAAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
26 7 0.17
27 26 0.63
28 5 0.12
29 3 0.07
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.42
Consensus pattern (26 bp):
TTCAAAATATTTAAAAAATTTTAAAA
Found at i:6071485 original size:84 final size:84
Alignment explanation
Indices: 6071324--6071492 Score: 284
Period size: 84 Copynumber: 2.0 Consensus size: 84
6071314 ATGTTATATC
*
6071324 TGTAATATCCCGAAAATTACTATAGTAAGAAAATAGGTATACTTGATATAGTAAAATAAGGAAAT
1 TGTAATATCCCGAAAATTACTACAGTAAGAAAATAGGTATACTTGATATAGTAAAATAAGGAAAT
**
6071389 AAAATGTTAAAAAACAAAA
66 AAAATGACAAAAAACAAAA
*
6071408 TGTAATATCCCGAAAATTACTACAGTAAGAAAGTAGGTATACTTGATATAGTAAAATAAGGAAAT
1 TGTAATATCCCGAAAATTACTACAGTAAGAAAATAGGTATACTTGATATAGTAAAATAAGGAAAT
* *
6071473 AAAGTGACAAAAAGCAAAA
66 AAAATGACAAAAAACAAAA
6071492 T
1 T
6071493 TTTGATTTAT
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
84 79 1.00
ACGTcount: A:0.52, C:0.08, G:0.15, T:0.25
Consensus pattern (84 bp):
TGTAATATCCCGAAAATTACTACAGTAAGAAAATAGGTATACTTGATATAGTAAAATAAGGAAAT
AAAATGACAAAAAACAAAA
Found at i:6071645 original size:21 final size:21
Alignment explanation
Indices: 6071595--6071642 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
6071585 GTAAATATTT
*
6071595 AAAATTTGAGGGGTTAAAGTG
1 AAAATTTGAGGGGTTAAAGTC
*
6071616 TAAATTTGAGGGGTTAAAG-C
1 AAAATTTGAGGGGTTAAAGTC
6071636 AAAATTT
1 AAAATTT
6071643 TGATTTATGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 6 0.25
21 18 0.75
ACGTcount: A:0.40, C:0.02, G:0.27, T:0.31
Consensus pattern (21 bp):
AAAATTTGAGGGGTTAAAGTC
Found at i:6073668 original size:86 final size:85
Alignment explanation
Indices: 6073571--6073742 Score: 226
Period size: 86 Copynumber: 2.0 Consensus size: 85
6073561 TTAATACAAT
* *
6073571 TAACAATTAATAATTTGATGTAATTTG-ATAATTTTACTAATAATTAAT-ACAATT-A-ACAATT
1 TAACAATTAATAA-TT-A-ATAATTTGAATAATTTGA-TAAT-ATTAATAACAATTAATACAATT
6073632 AATAATTTTACTAACAAAATGTTAG
61 AATAATTTTACTAACAAAATGTTAG
* *
6073657 TAACAATTAATAATTAATAATTTGATATAATTTGATAATTTTAGTAACAATTAATACAATTAATA
1 TAACAATTAATAATTAATAATTTGA-ATAATTTGATAATATTAATAACAATTAATACAATTAATA
6073722 ATTTTACTAACAAAATGTTAG
65 ATTTTACTAACAAAATGTTAG
6073743 ATTTTACAAA
Statistics
Matches: 77, Mismatches: 4, Indels: 10
0.85 0.04 0.11
Matches are distributed among these distances:
83 11 0.14
84 11 0.14
85 11 0.14
86 44 0.57
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (85 bp):
TAACAATTAATAATTAATAATTTGAATAATTTGATAATATTAATAACAATTAATACAATTAATAA
TTTTACTAACAAAATGTTAG
Found at i:6073767 original size:17 final size:17
Alignment explanation
Indices: 6073731--6073770 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
6073721 AATTTTACTA
*
6073731 ACAAAATGTTAGATTTT
1 ACAAAATGTTAGATTGT
6073748 ACAAAATGTT-GATTGGT
1 ACAAAATGTTAGATT-GT
6073765 ACAAAA
1 ACAAAA
6073771 AATATATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.45, C:0.07, G:0.15, T:0.33
Consensus pattern (17 bp):
ACAAAATGTTAGATTGT
Found at i:6073807 original size:16 final size:16
Alignment explanation
Indices: 6073788--6073844 Score: 87
Period size: 16 Copynumber: 3.6 Consensus size: 16
6073778 AATTTGATAC
*
6073788 AATTTTAATAATAATT
1 AATTTTAATAACAATT
*
6073804 AATTTTGATAACAATT
1 AATTTTAATAACAATT
6073820 AATTTTAATAACAATT
1 AATTTTAATAACAATT
*
6073836 AGTTTTAAT
1 AATTTTAAT
6073845 TTTAATAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.47
Consensus pattern (16 bp):
AATTTTAATAACAATT
Found at i:6073828 original size:22 final size:23
Alignment explanation
Indices: 6073818--6073879 Score: 90
Period size: 22 Copynumber: 2.7 Consensus size: 23
6073808 TTGATAACAA
* *
6073818 TTAATTTTAATAACAAT-TAGTT
1 TTAATTTTAATAAAAATATAATT
6073840 TTAATTTTAATAAAAATATAATT
1 TTAATTTTAATAAAAATATAATT
6073863 TTAATTTTAATTAAAAA
1 TTAATTTTAA-TAAAAA
6073880 ACGGGCCGGG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
22 16 0.44
23 14 0.39
24 6 0.17
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (23 bp):
TTAATTTTAATAAAAATATAATT
Found at i:6075561 original size:29 final size:29
Alignment explanation
Indices: 6075507--6075568 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
6075497 ATCAAAAATA
*
6075507 CCGATTTTAAGAAAAATGATCGGATTGGG
1 CCGATTTTAAGAAAAATGATCGGATTAGG
** *
6075536 CCGATTTTTTGAAAAATTA-CGAGATTAGG
1 CCGATTTTAAGAAAAATGATCG-GATTAGG
6075565 CCGA
1 CCGA
6075569 AAAAAGAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 2 0.07
29 26 0.93
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.29
Consensus pattern (29 bp):
CCGATTTTAAGAAAAATGATCGGATTAGG
Found at i:6081123 original size:36 final size:36
Alignment explanation
Indices: 6081057--6081199 Score: 232
Period size: 36 Copynumber: 3.9 Consensus size: 36
6081047 GATGCTTACG
* * *
6081057 AGAGGAAAATGGGATGTAAAACAGTATATCACTTATA
1 AGAGGAAAATGAGAT-TTAAACAGTTTATCACTTATA
6081094 AGAGGAAAATGAGATTTAAACAGTTTATCACTTATA
1 AGAGGAAAATGAGATTTAAACAGTTTATCACTTATA
*
6081130 AGAGGAAAATGAGATTTAAACAGTTTATCACTTACA
1 AGAGGAAAATGAGATTTAAACAGTTTATCACTTATA
6081166 AGAGGAAAATGAGATTTAAAACAGTTTATCACTT
1 AGAGGAAAATGAGATTT-AAACAGTTTATCACTT
6081200 CAGCAATTAT
Statistics
Matches: 101, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
36 71 0.70
37 30 0.30
ACGTcount: A:0.45, C:0.09, G:0.18, T:0.28
Consensus pattern (36 bp):
AGAGGAAAATGAGATTTAAACAGTTTATCACTTATA
Found at i:6083915 original size:57 final size:54
Alignment explanation
Indices: 6083818--6083948 Score: 158
Period size: 57 Copynumber: 2.4 Consensus size: 54
6083808 CAAATCATCA
* * *
6083818 AAAGATTCATTGATTCGATCTAGAAAAAAACCATCCGTTTCGTCATACACATCGTTG
1 AAAGATTTATTGATTCCATCTAGAAAAAAACCATCCGTTTCG---TACACATCATTG
* *
6083875 AAAGATTTATTGATTCCAT-TGAGAAAAAAGCCA-CTTGTTTCGTACACATCATTG
1 AAAGATTTATTGATTCCATCT-AGAAAAAAACCATC-CGTTTCGTACACATCATTG
6083929 AAAGATTTATTGATTCCATC
1 AAAGATTTATTGATTCCATC
6083949 GAGTAATATG
Statistics
Matches: 66, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
54 30 0.45
56 2 0.03
57 34 0.52
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (54 bp):
AAAGATTTATTGATTCCATCTAGAAAAAAACCATCCGTTTCGTACACATCATTG
Found at i:6084418 original size:21 final size:22
Alignment explanation
Indices: 6084380--6084420 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
6084370 ATTTTATCAG
*
6084380 AAAATTTGCCTTTAAAGATAAC
1 AAAAATTGCCTTTAAAGATAAC
*
6084402 AAAAATTG-CTTTTAAGATA
1 AAAAATTGCCTTTAAAGATA
6084421 TTAAAAACTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.34
Consensus pattern (22 bp):
AAAAATTGCCTTTAAAGATAAC
Found at i:6085855 original size:2 final size:2
Alignment explanation
Indices: 6085850--6085889 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
6085840 AATTATCCTT
6085850 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6085890 AAAACTAGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6118254 original size:34 final size:35
Alignment explanation
Indices: 6118177--6118300 Score: 164
Period size: 34 Copynumber: 3.5 Consensus size: 35
6118167 NGTAGCTTTA
*
6118177 GCTACACTTATTCTGATCAGAGACAAAAGTGATAAGT-
1 GCTACACTTA-TCTGATCAGA-A-ACAAGTGATAAGTG
6118214 GCTACACTTATCTGATCAGAAACAAGTGAT-AGTG
1 GCTACACTTATCTGATCAGAAACAAGTGATAAGTG
* *
6118248 GTTACACTTATCTGATCAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAGAAAC-AAGTGATAAGTG
6118284 GCTACAC-TATCTGATCA
1 GCTACACTTATCTGATCA
6118301 AGTGATAAAG
Statistics
Matches: 80, Mismatches: 4, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
33 3 0.04
34 29 0.36
35 18 0.22
36 20 0.25
37 10 0.12
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.27
Consensus pattern (35 bp):
GCTACACTTATCTGATCAGAAACAAGTGATAAGTG
Found at i:6118291 original size:36 final size:36
Alignment explanation
Indices: 6118177--6118320 Score: 197
Period size: 36 Copynumber: 4.0 Consensus size: 36
6118167 NGTAGCTTTA
6118177 GCTACACTTATTCTGATCAGAGACAAAAGTGATAAGT-
1 GCTACACTTA-TCTGATCAGAGAC-AAAGTGATAAGTG
*
6118214 GCTACACTTATCTGATCAGAAAC-AAGTGAT-AGTG
1 GCTACACTTATCTGATCAGAGACAAAGTGATAAGTG
*
6118248 GTTACACTTATCTGATCAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAGAGACAAAGTGATAAGTG
* *
6118284 GCTACAC-TATCTGATCAAGTGATAAAGTGATAAGTG
1 GCTACACTTATCTGATC-AGAGACAAAGTGATAAGTG
6118320 G
1 G
6118321 TAGCTTCAGC
Statistics
Matches: 97, Mismatches: 6, Indels: 9
0.87 0.05 0.08
Matches are distributed among these distances:
33 3 0.03
34 28 0.29
35 16 0.16
36 40 0.41
37 10 0.10
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.27
Consensus pattern (36 bp):
GCTACACTTATCTGATCAGAGACAAAGTGATAAGTG
Found at i:6118344 original size:46 final size:44
Alignment explanation
Indices: 6118284--6118406 Score: 178
Period size: 46 Copynumber: 2.8 Consensus size: 44
6118274 GTGATAAGTG
*
6118284 GCTACAC-TATCTGATCAAGTGATAAAGTGATAAGTGGTAGCTTCA
1 GCTACACTTATCTGATCAAGTGA-AAAGTGATAAGTGGTAGCCT-A
*
6118329 GCTACACTTATCTGATCAAGTGGCAAAGTGATAAGTGGTAGCCTA
1 GCTACACTTATCTGATCAAGT-GAAAAGTGATAAGTGGTAGCCTA
*
6118374 GCTACACTTATCTGATCAAG-GACAAGTGATAAG
1 GCTACACTTATCTGATCAAGTGAAAAGTGATAAG
6118407 AGGTCATATG
Statistics
Matches: 72, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
43 11 0.15
45 28 0.39
46 32 0.44
47 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (44 bp):
GCTACACTTATCTGATCAAGTGAAAAGTGATAAGTGGTAGCCTA
Found at i:6119783 original size:32 final size:31
Alignment explanation
Indices: 6119738--6119833 Score: 165
Period size: 31 Copynumber: 3.1 Consensus size: 31
6119728 CTTAGATAAT
6119738 TTTAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
*
6119769 TTTAAAGAGTTTTTATTAGGATTCAACTACTC
1 TTTAAAGAG-TTTTATTAGGATTCAATTACTC
*
6119801 TTGAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
6119832 TT
1 TT
6119834 GTAATTTGCC
Statistics
Matches: 61, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
31 32 0.52
32 29 0.48
ACGTcount: A:0.31, C:0.10, G:0.14, T:0.45
Consensus pattern (31 bp):
TTTAAAGAGTTTTATTAGGATTCAATTACTC
Found at i:6124371 original size:13 final size:13
Alignment explanation
Indices: 6124353--6124392 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
6124343 AGTAGAAGTG
*
6124353 ACAATTTTATTAA
1 ACAATTTTATCAA
*
6124366 ACAATTTTTATCAG
1 ACAA-TTTTATCAA
6124380 ACAATTTTATCAA
1 ACAATTTTATCAA
6124393 CCATAAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.42, C:0.12, G:0.03, T:0.42
Consensus pattern (13 bp):
ACAATTTTATCAA
Found at i:6136606 original size:21 final size:20
Alignment explanation
Indices: 6136567--6136603 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
6136557 AATTTTCAAT
6136567 TTTTATAAAACTGAATATTG
1 TTTTATAAAACTGAATATTG
6136587 TTTTATAAAA-TGAATAT
1 TTTTATAAAACTGAATAT
6136604 ATTTGAAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (20 bp):
TTTTATAAAACTGAATATTG
Found at i:6142140 original size:39 final size:38
Alignment explanation
Indices: 6142086--6142166 Score: 153
Period size: 39 Copynumber: 2.1 Consensus size: 38
6142076 AGTAAGAGTA
6142086 TTTAGATAGTTGCCAACTTGTGTGCAAAGACTTTAAGCT
1 TTTAGATAGTTGCCAACTTGTGTGCAAAGACTTTAAG-T
6142125 TTTAGATAGTTGCCAACTTGTGTGCAAAGACTTTAAGT
1 TTTAGATAGTTGCCAACTTGTGTGCAAAGACTTTAAGT
6142163 TTTA
1 TTTA
6142167 ATCATTTGCT
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
38 5 0.12
39 37 0.88
ACGTcount: A:0.28, C:0.14, G:0.20, T:0.38
Consensus pattern (38 bp):
TTTAGATAGTTGCCAACTTGTGTGCAAAGACTTTAAGT
Found at i:6158542 original size:12 final size:13
Alignment explanation
Indices: 6158512--6158554 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
6158502 TTTTATTTTT
6158512 AATTAAAACTATA
1 AATTAAAACTATA
6158525 AATTAAAA-TATA
1 AATTAAAACTATA
*
6158537 ATTTAAAAACTATCA
1 AATT-AAAACTAT-A
6158552 AAT
1 AAT
6158555 AAATTTTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 7 0.28
13 12 0.48
14 3 0.12
15 3 0.12
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (13 bp):
AATTAAAACTATA
Found at i:6167428 original size:22 final size:22
Alignment explanation
Indices: 6167400--6167458 Score: 91
Period size: 22 Copynumber: 2.7 Consensus size: 22
6167390 TTTATTGTTC
6167400 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTG
*
6167422 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTG
**
6167444 AGCCATGAGAGCTTA
1 AAACATGAGAGCTTA
6167459 CAAGAACAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.36, C:0.15, G:0.25, T:0.24
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTG
Found at i:6178844 original size:2 final size:2
Alignment explanation
Indices: 6178837--6178862 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6178827 ATGTTTTCTA
6178837 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
6178863 TTGACATGCA
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:6180313 original size:22 final size:22
Alignment explanation
Indices: 6180285--6180364 Score: 115
Period size: 22 Copynumber: 3.6 Consensus size: 22
6180275 CTTAACTACC
6180285 ACGTACTAAGCTCTCATGTTTA
1 ACGTACTAAGCTCTCATGTTTA
6180307 ACGTACTAAGCTCTCATGTTTA
1 ACGTACTAAGCTCTCATGTTTA
* * * **
6180329 ACGAACTAAACCCTCATGGCTA
1 ACGTACTAAGCTCTCATGTTTA
6180351 ACGTACTAAGCTCT
1 ACGTACTAAGCTCT
6180365 TATTCAACCA
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.30
Consensus pattern (22 bp):
ACGTACTAAGCTCTCATGTTTA
Found at i:6181660 original size:7 final size:7
Alignment explanation
Indices: 6181650--6181694 Score: 83
Period size: 7 Copynumber: 6.6 Consensus size: 7
6181640 ATAAAATAAA
6181650 AAATTAT
1 AAATTAT
6181657 AAATTAT
1 AAATTAT
6181664 AAATTAT
1 AAATTAT
6181671 AAATTAT
1 AAATTAT
6181678 AAATTAT
1 AAATTAT
6181685 AAATT-T
1 AAATTAT
6181691 AAAT
1 AAAT
6181695 ATTAATATAT
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 5 0.13
7 33 0.87
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
AAATTAT
Found at i:6181667 original size:21 final size:21
Alignment explanation
Indices: 6181633--6181688 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 21
6181623 AAATTTTGAT
6181633 TAAATTAATAAAATAAAAAATTA
1 TAAATT-AT-AAATAAAAAATTA
* *
6181656 TAAATTATAAATTATAAATTA
1 TAAATTATAAATAAAAAATTA
6181677 TAAATTATAAAT
1 TAAATTATAAAT
6181689 TTAAATATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
21 23 0.74
22 2 0.06
23 6 0.19
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
TAAATTATAAATAAAAAATTA
Found at i:6182008 original size:14 final size:14
Alignment explanation
Indices: 6181991--6182018 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
6181981 CTCACATTTC
6181991 TTTTCTTTTCTCCA
1 TTTTCTTTTCTCCA
6182005 TTTTCTTTTCTCCA
1 TTTTCTTTTCTCCA
6182019 GATTTCTGCT
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:0.07, C:0.29, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTTCTTTTCTCCA
Found at i:6182009 original size:19 final size:18
Alignment explanation
Indices: 6181971--6182015 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
6181961 TACGGTACGC
6181971 TTCTTTTC-TTCTCACAT
1 TTCTTTTCTTTCTCACAT
6181988 TTCTTTTCTTTTCTC-CATT
1 TTCTTTTC-TTTCTCACA-T
6182007 TTCTTTTCT
1 TTCTTTTCT
6182016 CCAGATTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 8 0.32
18 3 0.12
19 14 0.56
ACGTcount: A:0.07, C:0.27, G:0.00, T:0.67
Consensus pattern (18 bp):
TTCTTTTCTTTCTCACAT
Found at i:6183720 original size:12 final size:12
Alignment explanation
Indices: 6183703--6183727 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6183693 TTGCAGGCGC
6183703 AGTCTCCTAACT
1 AGTCTCCTAACT
6183715 AGTCTCCTAACT
1 AGTCTCCTAACT
6183727 A
1 A
6183728 CAATGCTACC
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:0.28, C:0.32, G:0.08, T:0.32
Consensus pattern (12 bp):
AGTCTCCTAACT
Found at i:6185035 original size:17 final size:18
Alignment explanation
Indices: 6185010--6185051 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
6185000 TATAAGAATA
*
6185010 ATTATATTA-AGAATTTT
1 ATTAAATTATAGAATTTT
* *
6185027 ATTAAATTATATATTTTT
1 ATTAAATTATAGAATTTT
6185045 ATTAAAT
1 ATTAAAT
6185052 GATATTTAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (18 bp):
ATTAAATTATAGAATTTT
Found at i:6185595 original size:19 final size:20
Alignment explanation
Indices: 6185568--6185613 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
6185558 TATTTTTAAA
* *
6185568 ATTTTAAAAATTAAAAAA-C
1 ATTTAAAAAAATAAAAAATC
6185587 ATTTAAAAAAATAAAAAATC
1 ATTTAAAAAAATAAAAAATC
6185607 A-TTAAAA
1 ATTTAAAA
6185614 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 22 0.92
20 2 0.08
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.28
Consensus pattern (20 bp):
ATTTAAAAAAATAAAAAATC
Found at i:6186058 original size:2 final size:2
Alignment explanation
Indices: 6186051--6186076 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6186041 GTCCGGGTGC
6186051 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
6186077 TGTATTTATA
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:6187838 original size:14 final size:14
Alignment explanation
Indices: 6187796--6187825 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
6187786 AGGTTGATTA
6187796 TTTTCTTCATATTC
1 TTTTCTTCATATTC
6187810 TTTTCTTCATATTC
1 TTTTCTTCATATTC
6187824 TT
1 TT
6187826 CATATTCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.13, C:0.20, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTTCTTCATATTC
Found at i:6193227 original size:43 final size:43
Alignment explanation
Indices: 6193166--6193269 Score: 190
Period size: 43 Copynumber: 2.4 Consensus size: 43
6193156 TTTGAGTACT
6193166 TCTAATCAGTGACAAGTGATAAGTGGTAGTTTAGCTACATTTA
1 TCTAATCAGTGACAAGTGATAAGTGGTAGTTTAGCTACATTTA
6193209 TCTAATCAGTGACAAGTGATAAGTGGTAGTTTAGCTACATTTA
1 TCTAATCAGTGACAAGTGATAAGTGGTAGTTTAGCTACATTTA
* *
6193252 TCTGATCAGTGATAAGTG
1 TCTAATCAGTGACAAGTG
6193270 GTAGCTTTAG
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
43 59 1.00
ACGTcount: A:0.32, C:0.12, G:0.22, T:0.35
Consensus pattern (43 bp):
TCTAATCAGTGACAAGTGATAAGTGGTAGTTTAGCTACATTTA
Found at i:6193270 original size:36 final size:37
Alignment explanation
Indices: 6193223--6193303 Score: 137
Period size: 37 Copynumber: 2.2 Consensus size: 37
6193213 ATCAGTGACA
*
6193223 AGTGATAAGTGGTAG-TTTAGCTACATTTATCTGATC
1 AGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATC
*
6193259 AGTGATAAGTGGTAGCTTTAGCTGCACTTATCTGATC
1 AGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATC
6193296 AGTGATAA
1 AGTGATAA
6193304 CTGACAAGTG
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
36 15 0.36
37 27 0.64
ACGTcount: A:0.28, C:0.12, G:0.23, T:0.36
Consensus pattern (37 bp):
AGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATC
Found at i:6193323 original size:87 final size:87
Alignment explanation
Indices: 6193218--6193438 Score: 336
Period size: 87 Copynumber: 2.5 Consensus size: 87
6193208 ATCTAATCAG
*
6193218 TGACAAGTGATAAGTGGTAG-TTTAGCTACATTTATCTGATCAGTGATAAGTGGTAGCTTTAGCT
1 TGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGATAAGTGGTAGC-TTAGCT
*
6193282 GCACTTATCTGATCAGTGATAAC
65 GCACTTATCTGATCAGTGACAAC
* * * *
6193305 TGACAAGTGATAAGTGGTAGCTTTAGTTGCACTTATTTGATCAGTGATAAGTGGTGGCTTAGCTG
1 TGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGATAAGTGGTAGCTTAGCTG
* *
6193370 CACTTATCTGATCGGTGACAAG
66 CACTTATCTGATCAGTGACAAC
* *
6193392 TGACAAGTGATAAGTGGTAGCTTTACCTACACTTATCTAATCAGTGA
1 TGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGA
6193439 CAACTGATAA
Statistics
Matches: 120, Mismatches: 13, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
87 88 0.73
88 32 0.27
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.33
Consensus pattern (87 bp):
TGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGATAAGTGGTAGCTTAGCTG
CACTTATCTGATCAGTGACAAC
Found at i:6193382 original size:36 final size:37
Alignment explanation
Indices: 6193310--6193393 Score: 116
Period size: 36 Copynumber: 2.3 Consensus size: 37
6193300 ATAACTGACA
* *
6193310 AGTGATAAGTGGTAGCTTTAGTTGCACTTATTTGATC
1 AGTGATAAGTGGTAGCTTTAGCTGCACTTATCTGATC
*
6193347 AGTGATAAGTGGTGGC-TTAGCTGCACTTATCTGATC
1 AGTGATAAGTGGTAGCTTTAGCTGCACTTATCTGATC
* *
6193383 GGTGACAAGTG
1 AGTGATAAGTG
6193394 ACAAGTGATA
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
36 27 0.64
37 15 0.36
ACGTcount: A:0.24, C:0.13, G:0.29, T:0.35
Consensus pattern (37 bp):
AGTGATAAGTGGTAGCTTTAGCTGCACTTATCTGATC
Done.