Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008959.1 Hibiscus syriacus cultivar Beakdansim tig00112293_pilon, 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: 4521124
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 18 of 21
Found at i:3675598 original size:17 final size:16
Alignment explanation
Indices: 3675567--3675600 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
3675557 CACGTGAGGA
3675567 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
3675583 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
3675600 T
1 T
3675601 ACTGTCTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:3676217 original size:37 final size:37
Alignment explanation
Indices: 3676171--3676435 Score: 292
Period size: 37 Copynumber: 7.2 Consensus size: 37
3676161 CTATTTCCAC
* *
3676171 AAAACTATATAATATATATTTTTTCAAAAATATTTTTA
1 AAAACTATATATTATATA-ATTTTCAAAAATATTTTTA
* * * *
3676209 AATA-TATATATTATATAATTTTAAAAAATGTTTTCA
1 AAAACTATATATTATATAATTTTCAAAAATATTTTTA
3676245 AAAACTATATATTATATAAGTTTTC-AAAATGA-TTTTA
1 AAAACTATATATTATATAA-TTTTCAAAAAT-ATTTTTA
* *
3676282 AAAACTATATATTATATATATTTTCTAAAAT-GTTTTA
1 AAAACTATATATTATATA-ATTTTCAAAAATATTTTTA
*
3676319 AAAACTATATATTATATAATTTTCAAAAAT-GTTTTA
1 AAAACTATATATTATATAATTTTCAAAAATATTTTTA
* * * * **
3676355 AAAACTATGTAATAAATATTTTTCAAAAATGCTTTT-
1 AAAACTATATATTATATAATTTTCAAAAATATTTTTA
*
3676391 AAAACTATATATTATATATATTTTCTAAAATA-TTTTA
1 AAAACTATATATTATATA-ATTTTCAAAAATATTTTTA
3676428 AAAACTAT
1 AAAACTAT
3676436 GAGAAAATAA
Statistics
Matches: 196, Mismatches: 22, Indels: 19
0.83 0.09 0.08
Matches are distributed among these distances:
36 80 0.41
37 103 0.53
38 13 0.07
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.45
Consensus pattern (37 bp):
AAAACTATATATTATATAATTTTCAAAAATATTTTTA
Found at i:3676269 original size:74 final size:73
Alignment explanation
Indices: 3676171--3676435 Score: 326
Period size: 73 Copynumber: 3.6 Consensus size: 73
3676161 CTATTTCCAC
* * * *
3676171 AAAACTATATAATATATATTTTTTCAAAAATATTTTTAAATA-TATATATTATATAATTTTAAAA
1 AAAACTATATATTATATA-ATTTTCAAAAATATTTTTAAAAACTATATATTATATAATTTTCAAA
3676235 AATGTTTTCA
65 AATGTTTT-A
*
3676245 AAAACTATATATTATATAAGTTTTC-AAAATGA-TTTTAAAAACTATATATTATATATATTTTCT
1 AAAACTATATATTATATAA-TTTTCAAAAAT-ATTTTTAAAAACTATATATTATATA-ATTTTCA
3676308 AAAATGTTTTA
63 AAAATGTTTTA
* * * * *
3676319 AAAACTATATATTATATAATTTTCAAAAAT-GTTTTAAAAACTATGTAATAAATATTTTTCAAAA
1 AAAACTATATATTATATAATTTTCAAAAATATTTTTAAAAACTATATATTATATAATTTTCAAAA
3676383 ATGCTTTT-
66 ATG-TTTTA
*
3676391 AAAACTATATATTATATATATTTTCTAAAATA-TTTTAAAAACTAT
1 AAAACTATATATTATATA-ATTTTCAAAAATATTTTTAAAAACTAT
3676436 GAGAAAATAA
Statistics
Matches: 171, Mismatches: 11, Indels: 19
0.85 0.05 0.09
Matches are distributed among these distances:
72 29 0.17
73 66 0.39
74 61 0.36
75 15 0.09
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.45
Consensus pattern (73 bp):
AAAACTATATATTATATAATTTTCAAAAATATTTTTAAAAACTATATATTATATAATTTTCAAAA
ATGTTTTA
Found at i:3676299 original size:111 final size:110
Alignment explanation
Indices: 3676171--3676435 Score: 376
Period size: 111 Copynumber: 2.4 Consensus size: 110
3676161 CTATTTCCAC
* * * *
3676171 AAAACTATATAATATATATTTTTTCAAAAATATTTTTAAATA-TATATATTATATAATTTTAAAA
1 AAAACTATATATTATATATATTTTCTAAAATATTTTTAAAAACTATATATTATATAATTTTAAAA
* *
3676235 AATGTTTTCAAAAACTATATATTATATAAGTTTTC-AAAATGATTTT
66 AATGTTTT-AAAAACTATATAATAAAT-AGTTTTCAAAAATGATTTT
* *
3676281 AAAAACTATATATTATATATATTTTCTAAAAT-GTTTTAAAAACTATATATTATATAATTTTCAA
1 -AAAACTATATATTATATATATTTTCTAAAATATTTTTAAAAACTATATATTATATAATTTTAAA
* * *
3676345 AAATGTTTTAAAAACTATGTAATAAATATTTTTCAAAAATGCTTTT
65 AAATGTTTTAAAAACTATATAATAAATAGTTTTCAAAAATGATTTT
3676391 AAAACTATATATTATATATATTTTCTAAAATA-TTTTAAAAACTAT
1 AAAACTATATATTATATATATTTTCTAAAATATTTTTAAAAACTAT
3676436 GAGAAAATAA
Statistics
Matches: 140, Mismatches: 11, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
109 50 0.36
110 33 0.24
111 57 0.41
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.45
Consensus pattern (110 bp):
AAAACTATATATTATATATATTTTCTAAAATATTTTTAAAAACTATATATTATATAATTTTAAAA
AATGTTTTAAAAACTATATAATAAATAGTTTTCAAAAATGATTTT
Found at i:3676649 original size:21 final size:21
Alignment explanation
Indices: 3676617--3676713 Score: 122
Period size: 21 Copynumber: 4.6 Consensus size: 21
3676607 GATTTACATA
*
3676617 TTCGCATTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
* **
3676638 TTTGCGTTGCGATAGTTGAAG
1 TTCGCGTTGCGATAGTCCAAG
** *
3676659 TTCGCGTTGCGATTTTCCAAA
1 TTCGCGTTGCGATAGTCCAAG
*
3676680 TTTGCGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
3676701 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
3676714 TTATTACAAA
Statistics
Matches: 61, Mismatches: 15, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 61 1.00
ACGTcount: A:0.19, C:0.20, G:0.27, T:0.35
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:3676669 original size:42 final size:42
Alignment explanation
Indices: 3676617--3676745 Score: 145
Period size: 42 Copynumber: 3.1 Consensus size: 42
3676607 GATTTACATA
* * **
3676617 TTCGCATTGCGATAGTCCAAGTTTGCGTTGCGATAGTTGAAG
1 TTCGCGTTGCGATAGTCCAAATTTGCGTTGCGATAGTCCAAG
**
3676659 TTCGCGTTGCGATTTTCCAAATTTGCGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAATTTGCGTTGCGATAGTCCAAG
* * *
3676701 TTCGCGTTGCGATTTATTACAAA-TT-CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGA--TAGTCCAAATTTGCGTTGCGATAGTCCAAG
3676743 TTC
1 TTC
3676746 TCTAAAAAGA
Statistics
Matches: 76, Mismatches: 9, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
42 67 0.88
43 2 0.03
44 7 0.09
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.36
Consensus pattern (42 bp):
TTCGCGTTGCGATAGTCCAAATTTGCGTTGCGATAGTCCAAG
Found at i:3677638 original size:42 final size:42
Alignment explanation
Indices: 3677576--3677765 Score: 335
Period size: 42 Copynumber: 4.5 Consensus size: 42
3677566 TGCGATTTTG
*
3677576 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
*
3677618 GACTATCGCAACGAGCTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
*
3677660 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTG
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
3677702 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
3677744 GACTATCGCAACGCGAACTTGG
1 GACTATCGCAA--CGAACTTGG
3677766 GCTATCGCAA
Statistics
Matches: 141, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
42 132 0.94
44 9 0.06
ACGTcount: A:0.34, C:0.25, G:0.21, T:0.19
Consensus pattern (42 bp):
GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
Found at i:3677670 original size:63 final size:61
Alignment explanation
Indices: 3677573--3677859 Score: 316
Period size: 63 Copynumber: 4.6 Consensus size: 61
3677563 CGTTGCGATT
* *
3677573 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAA-CGAGC
1 TTGGACTATCGCAACGAACTTGGAAT-AATCGCAACGCGAACTTCGACTATCGCAACCGAAC
* * * * *
3677634 TTGGAATAAATCGCAACGCGAACTTCGACT-ATCGCAA--CGAACTTGGAATAAATCGCAACGCG
1 TTGGACT--ATCGCAA--CGAACTTGGAATAATCGCAACGCGAACTTCGACT--ATCGCAAC-CG
3677696 AAC
59 AAC
3677699 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGCGAAC
1 TTGGACTATCGCAACGAACTTGGAAT-AATCGCAACGCGAACTTCGACTATCGCAAC-CGAAC
* *
3677762 TTGGGCTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAA-CGAAC
1 TTGGACTATCGCAACGAACTTGGAAT-AATCGCAACGCGAACTTCGACTATCGCAACCGAAC
* *
3677823 TTGGACTATCGTAACGCGAACTTGGACT-ATCGCAACG
1 TTGGACTATCGCAA--CGAACTTGGAATAATCGCAACG
3677860 AATTTGGAAA
Statistics
Matches: 194, Mismatches: 18, Indels: 28
0.81 0.08 0.12
Matches are distributed among these distances:
61 52 0.27
63 113 0.58
65 29 0.15
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.21
Consensus pattern (61 bp):
TTGGACTATCGCAACGAACTTGGAATAATCGCAACGCGAACTTCGACTATCGCAACCGAAC
Found at i:3677814 original size:21 final size:21
Alignment explanation
Indices: 3677573--3677859 Score: 274
Period size: 21 Copynumber: 13.8 Consensus size: 21
3677563 CGTTGCGATT
*
3677573 TTGGACTATCGCAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
*
3677592 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
* *
3677615 TTCGACTATCGCAA--CGAGC
1 TTGGACTATCGCAACGCGAAC
*
3677634 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
*
3677657 TTCGACTATCGCAA--CGAAC
1 TTGGACTATCGCAACGCGAAC
*
3677676 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
3677699 TTGGACTATCGCAA--CGAAC
1 TTGGACTATCGCAACGCGAAC
*
3677718 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
*
3677741 TTCGACTATCGCAACGCGAAC
1 TTGGACTATCGCAACGCGAAC
* *
3677762 TTGGGCTATCGCAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
*
3677781 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
*
3677804 TTCGACTATCGCAA--CGAAC
1 TTGGACTATCGCAACGCGAAC
*
3677823 TTGGACTATCGTAACGCGAAC
1 TTGGACTATCGCAACGCGAAC
3677844 TTGGACTATCGCAACG
1 TTGGACTATCGCAACG
3677860 AATTTGGAAA
Statistics
Matches: 219, Mismatches: 27, Indels: 42
0.76 0.09 0.15
Matches are distributed among these distances:
19 62 0.28
21 109 0.50
23 48 0.22
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.21
Consensus pattern (21 bp):
TTGGACTATCGCAACGCGAAC
Found at i:3677900 original size:21 final size:21
Alignment explanation
Indices: 3677871--3677923 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
3677861 ATTTGGAAAA
*
3677871 TCGCATTGCGATAGTCGAAGT
1 TCGCGTTGCGATAGTCGAAGT
*
3677892 TCGCGTTGCGATAGTCGATGT
1 TCGCGTTGCGATAGTCGAAGT
*
3677913 TCGTGTTGCGA
1 TCGCGTTGCGA
3677924 ATCTGGAAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.17, C:0.19, G:0.32, T:0.32
Consensus pattern (21 bp):
TCGCGTTGCGATAGTCGAAGT
Found at i:3678364 original size:2 final size:2
Alignment explanation
Indices: 3678357--3678381 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3678347 CAACCCTTTC
3678357 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
3678382 CCTCCCCCTC
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:3681585 original size:19 final size:19
Alignment explanation
Indices: 3681561--3681628 Score: 55
Period size: 19 Copynumber: 3.5 Consensus size: 19
3681551 TTGTAGATTG
3681561 ATATATTATTTTTATTAGT
1 ATATATTATTTTTATTAGT
* ** *
3681580 ATATATTGGTTGTAGATTGGT
1 ATATATT-ATT-TTTATTAGT
* * *
3681601 GTATATTGTTTTTATTAGC
1 ATATATTATTTTTATTAGT
3681620 ATATATTAT
1 ATATATTAT
3681629 AATGTGCTGC
Statistics
Matches: 36, Mismatches: 11, Indels: 4
0.71 0.22 0.08
Matches are distributed among these distances:
19 19 0.53
20 5 0.14
21 12 0.33
ACGTcount: A:0.28, C:0.01, G:0.15, T:0.56
Consensus pattern (19 bp):
ATATATTATTTTTATTAGT
Found at i:3681589 original size:38 final size:40
Alignment explanation
Indices: 3681547--3681626 Score: 119
Period size: 40 Copynumber: 2.0 Consensus size: 40
3681537 AATAAGTTCT
*
3681547 TTGGTTGTAGATT-G-ATATATTATTTTTATTAGTATATA
1 TTGGTTGTAGATTGGTATATATTATTTTTATTAGCATATA
* *
3681585 TTGGTTGTAGATTGGTGTATATTGTTTTTATTAGCATATA
1 TTGGTTGTAGATTGGTATATATTATTTTTATTAGCATATA
3681625 TT
1 TT
3681627 ATAATGTGCT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
38 13 0.35
39 1 0.03
40 23 0.62
ACGTcount: A:0.25, C:0.01, G:0.19, T:0.55
Consensus pattern (40 bp):
TTGGTTGTAGATTGGTATATATTATTTTTATTAGCATATA
Found at i:3689422 original size:26 final size:27
Alignment explanation
Indices: 3689392--3689445 Score: 101
Period size: 26 Copynumber: 2.0 Consensus size: 27
3689382 ATATTAGAAA
3689392 CCCGAAATGGAACTCA-TTTCAACAAG
1 CCCGAAATGGAACTCATTTTCAACAAG
3689418 CCCGAAATGGAACTCATTTTCAACAAG
1 CCCGAAATGGAACTCATTTTCAACAAG
3689445 C
1 C
3689446 TTTACTTCCT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 16 0.59
27 11 0.41
ACGTcount: A:0.37, C:0.28, G:0.15, T:0.20
Consensus pattern (27 bp):
CCCGAAATGGAACTCATTTTCAACAAG
Found at i:3690802 original size:24 final size:24
Alignment explanation
Indices: 3690772--3690822 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
3690762 ATAAGAAAAC
* *
3690772 AACAAAGATGAGGTTTAGTTCAAA
1 AACAAAGACGAGGTTTAGGTCAAA
3690796 AACAAAGACGAGGTTTAGGTCAAA
1 AACAAAGACGAGGTTTAGGTCAAA
3690820 AAC
1 AAC
3690823 TCAAACTCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.47, C:0.12, G:0.22, T:0.20
Consensus pattern (24 bp):
AACAAAGACGAGGTTTAGGTCAAA
Found at i:3696273 original size:7 final size:7
Alignment explanation
Indices: 3696238--3696321 Score: 56
Period size: 7 Copynumber: 12.9 Consensus size: 7
3696228 CTTTACATTG
3696238 AACCCTA
1 AACCCTA
*
3696245 AAACCT-
1 AACCCTA
3696251 AACCCTA
1 AACCCTA
***
3696258 AATTTTA
1 AACCCTA
3696265 AACCCTA
1 AACCCTA
3696272 AACCCTA
1 AACCCTA
3696279 AA--CTA
1 AACCCTA
*
3696284 AA-ACTA
1 AACCCTA
3696290 AA-CCTA
1 AACCCTA
*
3696296 AA-CATA
1 AACCCTA
3696302 AACCCT-
1 AACCCTA
3696308 AACCACTA
1 AACC-CTA
3696316 AACCCT
1 AACCCT
3696322 TAATCCAATT
Statistics
Matches: 61, Mismatches: 11, Indels: 10
0.74 0.13 0.12
Matches are distributed among these distances:
5 5 0.08
6 24 0.39
7 28 0.46
8 4 0.07
ACGTcount: A:0.48, C:0.33, G:0.00, T:0.19
Consensus pattern (7 bp):
AACCCTA
Found at i:3696292 original size:18 final size:18
Alignment explanation
Indices: 3696269--3696303 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
3696259 ATTTTAAACC
3696269 CTAAACCCTAAAC-TAAAA
1 CTAAA-CCTAAACATAAAA
3696287 CTAAACCTAAACATAAA
1 CTAAACCTAAACATAAA
3696304 CCCTAACCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.57, C:0.26, G:0.00, T:0.17
Consensus pattern (18 bp):
CTAAACCTAAACATAAAA
Found at i:3697991 original size:26 final size:26
Alignment explanation
Indices: 3697960--3698043 Score: 93
Period size: 26 Copynumber: 3.3 Consensus size: 26
3697950 TTAAATTAAA
3697960 TAAAATAAAATAATAATTGTAAATAT
1 TAAAATAAAATAATAATTGTAAATAT
** * * *
3697986 TAAAATAATTTGTATTATT-TAAA-AA
1 TAAAATAAAAT-AATAATTGTAAATAT
3698011 T-AAATAAAATAATAATTGTAAATAT
1 TAAAATAAAATAATAATTGTAAATAT
3698036 TAAAATAA
1 TAAAATAA
3698044 TTAAATATAA
Statistics
Matches: 44, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
23 5 0.11
24 11 0.25
25 4 0.09
26 19 0.43
27 5 0.11
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.37
Consensus pattern (26 bp):
TAAAATAAAATAATAATTGTAAATAT
Found at i:3697992 original size:18 final size:18
Alignment explanation
Indices: 3697971--3698045 Score: 63
Period size: 18 Copynumber: 4.4 Consensus size: 18
3697961 AAAATAAAAT
3697971 AATAATTGTAAATATTAA
1 AATAATTGTAAATATTAA
* *
3697989 AATAATTTGT-ATTATTTA
1 AATAA-TTGTAAATATTAA
*
3698007 AA-AA---TAAATA-AAA
1 AATAATTGTAAATATTAA
3698020 TAATAATTGTAAATATTAA
1 -AATAATTGTAAATATTAA
3698039 AATAATT
1 AATAATT
3698046 AAATATAAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 16
0.66 0.09 0.25
Matches are distributed among these distances:
13 2 0.05
14 5 0.12
15 2 0.05
17 2 0.05
18 26 0.60
19 6 0.14
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (18 bp):
AATAATTGTAAATATTAA
Found at i:3698054 original size:22 final size:21
Alignment explanation
Indices: 3698015--3698055 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
3698005 TAAAAATAAA
* *
3698015 TAAAATAATAATTGTAAATAT
1 TAAAATAATAAATATAAATAT
3698036 TAAAATAATTAAATATAAAT
1 TAAAATAA-TAAATATAAAT
3698056 CAATATATGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (21 bp):
TAAAATAATAAATATAAATAT
Found at i:3698060 original size:18 final size:19
Alignment explanation
Indices: 3698011--3698060 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 19
3698001 TATTTAAAAA
3698011 TAAATA-AAATAATAATTG
1 TAAATATAAATAATAATTG
*
3698029 TAAATATTAA-AATAA-T-
1 TAAATATAAATAATAATTG
3698045 TAAATATAAATCAATA
1 TAAATATAAAT-AATA
3698061 TATGTAGAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
16 9 0.33
17 1 0.04
18 15 0.56
19 2 0.07
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (19 bp):
TAAATATAAATAATAATTG
Found at i:3718991 original size:35 final size:35
Alignment explanation
Indices: 3718945--3719020 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
3718935 CCAACAAAGA
* *
3718945 AGAGTTTGATTAGGACTCAAATACTAGTCTAGAAT
1 AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
*
3718980 AGAGTTGGATTAGGACTCAAATACTAGTTTAAAAT
1 AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
3719015 AGAGTT
1 AGAGTT
3719021 TTTTTAGTAC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.38, C:0.09, G:0.21, T:0.32
Consensus pattern (35 bp):
AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
Found at i:3719535 original size:2 final size:2
Alignment explanation
Indices: 3719528--3719552 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3719518 TACTTTATTT
3719528 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
3719553 TTACTTTGAT
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:3719623 original size:18 final size:18
Alignment explanation
Indices: 3719584--3719628 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
3719574 TTATAATTTC
* *
3719584 TTTTATTTCTTTTTTTTA
1 TTTTATTACTATTTTTTA
3719602 -TTTATTACTATTTTTTA
1 TTTTATTACTATTTTTTA
*
3719619 TTTTAATACT
1 TTTTATTACT
3719629 TATTATTACT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 15 0.65
18 8 0.35
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (18 bp):
TTTTATTACTATTTTTTA
Found at i:3720564 original size:13 final size:13
Alignment explanation
Indices: 3720543--3720581 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
3720533 TTCATCTAAG
*
3720543 GCTCTAAACCC-T
1 GCTCCAAACCCGT
3720555 AGCTCCAAACCCGT
1 -GCTCCAAACCCGT
3720569 GCTCCAAACCCGT
1 GCTCCAAACCCGT
3720582 TTTATGTGGG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 23 0.96
14 1 0.04
ACGTcount: A:0.26, C:0.44, G:0.13, T:0.18
Consensus pattern (13 bp):
GCTCCAAACCCGT
Found at i:3726120 original size:9 final size:9
Alignment explanation
Indices: 3726106--3726134 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
3726096 AGGGCGCCCT
3726106 AAATTGAAA
1 AAATTGAAA
3726115 AAATTGAAA
1 AAATTGAAA
3726124 AAATTGAAA
1 AAATTGAAA
3726133 AA
1 AA
3726135 GAGAAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.69, C:0.00, G:0.10, T:0.21
Consensus pattern (9 bp):
AAATTGAAA
Found at i:3727259 original size:109 final size:109
Alignment explanation
Indices: 3727068--3727514 Score: 745
Period size: 109 Copynumber: 4.1 Consensus size: 109
3727058 GGGCCATCCA
* * *
3727068 TGATTTCAACCCCACGACGGAGGATATCGTACTACCCGAGA-ATACACAAGTTGAACTTCACAAC
1 TGATTTCAACTCCACGACGGAGGATATCGTGCTACCCGAGACA-ACACAAGTTCAACTTCACAAC
* * *
3727132 GAAGGGATGGCTGGTTGTCGACAAACAACTTCCCAATTTCAGAGC
65 GAAGGGACGACTGGTTGTCAACAAACAACTTCCCAATTTCAGAGC
*
3727177 TGATTTCAACTCCACGAAGGAGGATATCGTGCTACCCGAGACAACACAAGTTCAACTTCACAACG
1 TGATTTCAACTCCACGACGGAGGATATCGTGCTACCCGAGACAACACAAGTTCAACTTCACAACG
3727242 AAGGGACGACTGGTTGTCAACAAACAACTTCCCAATTTCAGAGC
66 AAGGGACGACTGGTTGTCAACAAACAACTTCCCAATTTCAGAGC
*
3727286 TGATTTCAACTCCACGACGGAGGATATCGTGCTACCCGAGACAACACAAGTTCAACTTCACAATG
1 TGATTTCAACTCCACGACGGAGGATATCGTGCTACCCGAGACAACACAAGTTCAACTTCACAACG
3727351 AAGGGACGACTGGTTGTCAACAAACAACTTCCCAATTTCAGAGC
66 AAGGGACGACTGGTTGTCAACAAACAACTTCCCAATTTCAGAGC
* * *
3727395 CGATTTTAACTCCACGGCGGAGGATATCGTGCTACCCGAGACAACACAAGTTCAACTTCACAACG
1 TGATTTCAACTCCACGACGGAGGATATCGTGCTACCCGAGACAACACAAGTTCAACTTCACAACG
**
3727460 AAGGGACGGTTGGTTGTCAACAAACAACTTCCCAATTTCAGAG-
66 AAGGGACGACTGGTTGTCAACAAACAACTTCCCAATTTCAGAGC
3727503 TCGATTTCAACT
1 T-GATTTCAACT
3727515 TGTATTGGAT
Statistics
Matches: 319, Mismatches: 17, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
109 318 1.00
110 1 0.00
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.21
Consensus pattern (109 bp):
TGATTTCAACTCCACGACGGAGGATATCGTGCTACCCGAGACAACACAAGTTCAACTTCACAACG
AAGGGACGACTGGTTGTCAACAAACAACTTCCCAATTTCAGAGC
Found at i:3728017 original size:35 final size:35
Alignment explanation
Indices: 3727967--3728038 Score: 126
Period size: 35 Copynumber: 2.1 Consensus size: 35
3727957 CCAACAAAGA
*
3727967 AGAGTTGGATCAGGACTCAAATACTAGTCTAGAAT
1 AGAGTTGGATCAGGACTCAAATACTAGTCTAAAAT
*
3728002 AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
1 AGAGTTGGATCAGGACTCAAATACTAGTCTAAAAT
3728037 AG
1 AG
3728039 GGTTTTTTAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.39, C:0.12, G:0.22, T:0.26
Consensus pattern (35 bp):
AGAGTTGGATCAGGACTCAAATACTAGTCTAAAAT
Found at i:3728539 original size:22 final size:23
Alignment explanation
Indices: 3728506--3728561 Score: 57
Period size: 22 Copynumber: 2.5 Consensus size: 23
3728496 TGTTTACTTA
3728506 TATTTCCA-TTATTA-TTATTATT
1 TATTT-CATTTATTACTTATTATT
*
3728528 TATTTCATTTA-TACTTTATTTTT
1 TATTTCATTTATTAC-TTATTATT
3728551 TATTT-ATTTAT
1 TATTTCATTTAT
3728562 ATATATATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
21 4 0.14
22 13 0.45
23 12 0.41
ACGTcount: A:0.25, C:0.07, G:0.00, T:0.68
Consensus pattern (23 bp):
TATTTCATTTATTACTTATTATT
Found at i:3728552 original size:23 final size:22
Alignment explanation
Indices: 3728520--3728562 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
3728510 TCCATTATTA
3728520 TTATTATTTATTTCATTTATACT
1 TTATTATTTATTT-ATTTATACT
*
3728543 TTATTTTTTATTTATTTATA
1 TTATTATTTATTTATTTATA
3728563 TATATATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.70
Consensus pattern (22 bp):
TTATTATTTATTTATTTATACT
Found at i:3728566 original size:26 final size:29
Alignment explanation
Indices: 3728514--3728566 Score: 76
Period size: 27 Copynumber: 1.9 Consensus size: 29
3728504 TATATTTCCA
*
3728514 TTATTATTATTATTTATTTCATTTATACT
1 TTATTATTATTATTTATTTCATATATACT
3728543 TTATT-TT-TTATTTATTT-ATATATA
1 TTATTATTATTATTTATTTCATATATA
3728567 TATATATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 6 0.26
27 10 0.43
28 2 0.09
29 5 0.22
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (29 bp):
TTATTATTATTATTTATTTCATATATACT
Found at i:3728625 original size:22 final size:22
Alignment explanation
Indices: 3728600--3728648 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
3728590 TTTCATATTC
* *
3728600 TTTATAATTTCTT-TTATTTCTT
1 TTTATAATTTATTACTATTT-TT
*
3728622 TTTATTATTTATTACTATTTTT
1 TTTATAATTTATTACTATTTTT
3728644 TTTAT
1 TTTAT
3728649 TTTAATACTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.73
Consensus pattern (22 bp):
TTTATAATTTATTACTATTTTT
Found at i:3728652 original size:20 final size:23
Alignment explanation
Indices: 3728614--3728657 Score: 58
Period size: 20 Copynumber: 2.0 Consensus size: 23
3728604 TAATTTCTTT
*
3728614 TATTTCTTTTTATTATTTATTAC
1 TATTTCTTTTTATTATTTAATAC
3728637 TATTT-TTTTTA-T-TTTAATAC
1 TATTTCTTTTTATTATTTAATAC
3728657 T
1 T
3728658 TATTATTACT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 8 0.40
21 1 0.05
22 6 0.30
23 5 0.25
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (23 bp):
TATTTCTTTTTATTATTTAATAC
Found at i:3736141 original size:41 final size:41
Alignment explanation
Indices: 3736096--3736291 Score: 277
Period size: 41 Copynumber: 4.8 Consensus size: 41
3736086 TGCTATTATC
* * *
3736096 GAATTAAGTTGAATTGTGAATTATTGCATGCTGCCATGATT
1 GAATTGAGTCGAATTGTGAATTATTGCATGCTTCCATGATT
*
3736137 GAATTGAGTCGAATTGTGAATTATTGCATGCTTCCATGATC
1 GAATTGAGTCGAATTGTGAATTATTGCATGCTTCCATGATT
*
3736178 GAATTGAGTCAAATTGTGAATTATTGCATGCTTCCATGATT
1 GAATTGAGTCGAATTGTGAATTATTGCATGCTTCCATGATT
* *
3736219 GAATTGAGTCGAATGGTGAATTATTGCATG-TTCTATGATTT
1 GAATTGAGTCGAATTGTGAATTATTGCATGCTTCCATGA-TT
* * * *
3736260 GAATTGAATTGAATTTTGAATTACTGCATGCT
1 GAATTGAGTCGAATTGTGAATTATTGCATGCT
3736292 GCCAAGATCG
Statistics
Matches: 139, Mismatches: 14, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
40 7 0.05
41 131 0.94
42 1 0.01
ACGTcount: A:0.29, C:0.11, G:0.21, T:0.39
Consensus pattern (41 bp):
GAATTGAGTCGAATTGTGAATTATTGCATGCTTCCATGATT
Found at i:3737225 original size:22 final size:22
Alignment explanation
Indices: 3737200--3737251 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
3737190 TAAGTTGTTT
*
3737200 ATGAAATGTACCTAAGAACTTA
1 ATGAAATATACCTAAGAACTTA
*
3737222 ATGAAATATACCTAAGAATTTA
1 ATGAAATATACCTAAGAACTTA
3737244 ATGAAATA
1 ATGAAATA
3737252 GTATAGTCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.50, C:0.10, G:0.12, T:0.29
Consensus pattern (22 bp):
ATGAAATATACCTAAGAACTTA
Found at i:3740574 original size:36 final size:36
Alignment explanation
Indices: 3740517--3740730 Score: 259
Period size: 36 Copynumber: 5.9 Consensus size: 36
3740507 GTGCGCTACA
*
3740517 TCCTTCCGTTCAACTTGAATCGGAAGTGCCGATGCT
1 TCCTTCCGTTCCACTTGAATCGGAAGTGCCGATGCT
* * * * *
3740553 TCATTCCGTTCGACTTAAATCGGAAGTGCCAATACT
1 TCCTTCCGTTCCACTTGAATCGGAAGTGCCGATGCT
* * * *
3740589 TCCTTCCGCTCGACTTGAATCAGAAGTGTCGATG-T
1 TCCTTCCGTTCCACTTGAATCGGAAGTGCCGATGCT
* *
3740624 CTCCTTCCGTTCCTCTTGAATCGGAAGTGCCGATGCC
1 -TCCTTCCGTTCCACTTGAATCGGAAGTGCCGATGCT
* * * *
3740661 TCCTTTCGTTCCTCTTGAATCGGAAGTGCCAATGCC
1 TCCTTCCGTTCCACTTGAATCGGAAGTGCCGATGCT
*
3740697 TCCTTCCGTTCCTCTTGAATCGGAAGTGCCGATG
1 TCCTTCCGTTCCACTTGAATCGGAAGTGCCGATG
3740731 AAATCACAAA
Statistics
Matches: 154, Mismatches: 22, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
35 1 0.01
36 153 0.99
ACGTcount: A:0.19, C:0.29, G:0.21, T:0.31
Consensus pattern (36 bp):
TCCTTCCGTTCCACTTGAATCGGAAGTGCCGATGCT
Found at i:3740714 original size:108 final size:108
Alignment explanation
Indices: 3740517--3740730 Score: 293
Period size: 108 Copynumber: 2.0 Consensus size: 108
3740507 GTGCGCTACA
* *
3740517 TCCTTCCGTTCAACTTGAATCGGAAGTGCCGATGCTTCATTCCGTTCGACTTAAATCGGAAGTGC
1 TCCTTCCGTTCAACTTGAATCGGAAGTGCCGATGCCTCATTCCGTTCCACTTAAATCGGAAGTGC
* * *
3740582 CAATACTTCCTTCCGCTCGACTTGAATCAGAAGTGTCGATGTC
66 CAATACCTCCTTCCGCTCCACTTGAATCAGAAGTGCCGATGTC
** * * * *
3740625 TCCTTCCGTTCCTCTTGAATCGGAAGTGCCGATGCCTCCTTTCGTTCCTCTTGAATCGGAAGTGC
1 TCCTTCCGTTCAACTTGAATCGGAAGTGCCGATGCCTCATTCCGTTCCACTTAAATCGGAAGTGC
* * * *
3740690 CAATGCCTCCTTCCGTTCCTCTTGAATCGGAAGTGCCGATG
66 CAATACCTCCTTCCGCTCCACTTGAATCAGAAGTGCCGATG
3740731 AAATCACAAA
Statistics
Matches: 91, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
108 91 1.00
ACGTcount: A:0.19, C:0.29, G:0.21, T:0.31
Consensus pattern (108 bp):
TCCTTCCGTTCAACTTGAATCGGAAGTGCCGATGCCTCATTCCGTTCCACTTAAATCGGAAGTGC
CAATACCTCCTTCCGCTCCACTTGAATCAGAAGTGCCGATGTC
Found at i:3744720 original size:43 final size:43
Alignment explanation
Indices: 3744671--3744813 Score: 198
Period size: 43 Copynumber: 3.3 Consensus size: 43
3744661 AGGTCGAGAC
* * * *
3744671 ATTTAGCAGCTTTTGTCTTTGA-AAACGTCGCTATTGACTGTGT
1 ATTTAGCGGCATTTATCTTT-ACAAACGCCGCTATTGACTGTGT
* *
3744714 ATTTAGCGGCGTTTATCTTTACAAACGCCGCTAGTGACTGTGT
1 ATTTAGCGGCATTTATCTTTACAAACGCCGCTATTGACTGTGT
* *
3744757 ATTTAGCGGCATTTATCTTTACAAATGCCGCTATTGACTATGT
1 ATTTAGCGGCATTTATCTTTACAAACGCCGCTATTGACTGTGT
3744800 ATTTAGCGGCATTT
1 ATTTAGCGGCATTT
3744814 GTAATTAAAA
Statistics
Matches: 90, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
42 1 0.01
43 89 0.99
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.39
Consensus pattern (43 bp):
ATTTAGCGGCATTTATCTTTACAAACGCCGCTATTGACTGTGT
Found at i:3744830 original size:43 final size:43
Alignment explanation
Indices: 3744671--3744830 Score: 194
Period size: 43 Copynumber: 3.7 Consensus size: 43
3744661 AGGTCGAGAC
* * * * *
3744671 ATTTAGCAGCTTTTGTCTTTGAAAACGTCGCTATTGACTGTGT
1 ATTTAGCGGCATTTATCTTTAAAAACGCCGCTATTGACTGTGT
* * *
3744714 ATTTAGCGGCGTTTATCTTTACAAACGCCGCTAGTGACTGTGT
1 ATTTAGCGGCATTTATCTTTAAAAACGCCGCTATTGACTGTGT
* * *
3744757 ATTTAGCGGCATTTATCTTTACAAATGCCGCTATTGACTATGT
1 ATTTAGCGGCATTTATCTTTAAAAACGCCGCTATTGACTGTGT
* **
3744800 ATTTAGCGGCATTTGTAATTAAAAACGCCGC
1 ATTTAGCGGCATTTATCTTTAAAAACGCCGC
3744831 AAATATGCCC
Statistics
Matches: 101, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 101 1.00
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.37
Consensus pattern (43 bp):
ATTTAGCGGCATTTATCTTTAAAAACGCCGCTATTGACTGTGT
Found at i:3755089 original size:16 final size:16
Alignment explanation
Indices: 3755068--3755108 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 16
3755058 AAAATGTTGA
3755068 AAAAAAAATAGCAGTTCG
1 AAAAAAAA-A-CAGTTCG
*
3755086 AAAAAAAAACTGTTCG
1 AAAAAAAAACAGTTCG
3755102 AAAAAAA
1 AAAAAAA
3755109 GACATGAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 13 0.59
17 1 0.05
18 8 0.36
ACGTcount: A:0.63, C:0.10, G:0.12, T:0.15
Consensus pattern (16 bp):
AAAAAAAAACAGTTCG
Found at i:3758509 original size:165 final size:164
Alignment explanation
Indices: 3758151--3758655 Score: 497
Period size: 165 Copynumber: 3.1 Consensus size: 164
3758141 TTATAAACTT
* * * * * * *
3758151 GCGGCGTTTGTAAACACAAACGTCACTAAAGCACAAGTCTATAGCGGTGTTTGTATAAGAACACC
1 GCGGCGTTTGTAAACACAAATGCCACTAAATCACGAGTCTATAGCGGCGTTTGTATAAAAACGCC
* ** * * * *
3758216 ACTAAAGTATGAGTCGCTAGCGGCATTTGTATAAAAGCGCCACTAAAGTACGAGTCTTTAGTGAC
66 ACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAACGCCACTAAAGTA-GAGTCTTTAGCGGC
* *
3758281 GTTTGTATAAAAACCCACTAAAGTATGAGTCTATA
130 ATTTTTATAAAAACCCACTAAAGTATGAGTCTATA
* * *
3758316 GTGGCGTTTGTAAACACAAATACCACTAAATCACGAGTCTATAGCGACGTTTGTATAAAAACGCC
1 GCGGCGTTTGTAAACACAAATGCCACTAAATCACGAGTCTATAGCGGCGTTTGTATAAAAACGCC
* * *
3758381 ACTAAAGGTACGAGTCTTTAGTGGTGTTTGTATAAAAACGCCACTAAATTATGAGTCTTTAGCGG
66 ACTAAA-GTACGAGTCTTTAGCGGCGTTTGTATAAAAACGCCACTAAAGTA-GAGTCTTTAGCGG
*
3758446 CATTTTTATAAAAACACCAC-AAAGGTACT-AG-CTTTTA
129 CATTTTTATAAAAAC-CCACTAAA-GTA-TGAGTC-TATA
* * * * * *
3758483 GCGGCGTTTGTATA-A-AAATGCCACTAAAAT-ATGATTCTATAGTGGCCTTTGTATAAAAATGC
1 GCGGCGTTTGTAAACACAAATGCCACT-AAATCACGAGTCTATAGCGGCGTTTGTATAAAAACGC
** * * *
3758545 GTCTAAAGTAC-AGTCTTTAGCGACGCTTT-TATAGAAACGCCACTAAAGTACAGTCTTTAGCGG
65 CACTAAAGTACGAGTCTTTAGCGGCG-TTTGTATAAAAACGCCACTAAAGTAGAGTCTTTAGCGG
* * * *
3758608 CATTTTTATAGAAACGCCGCTAAAATACT-AGTCTTTA
129 CATTTTTATAAAAAC-CCACTAAAGTA-TGAGTCTATA
*
3758645 GAGGCGTTTGT
1 GCGGCGTTTGT
3758656 TCTAAAAACG
Statistics
Matches: 285, Mismatches: 46, Indels: 21
0.81 0.13 0.06
Matches are distributed among these distances:
162 49 0.17
163 34 0.12
164 7 0.02
165 101 0.35
166 69 0.24
167 24 0.08
168 1 0.00
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.29
Consensus pattern (164 bp):
GCGGCGTTTGTAAACACAAATGCCACTAAATCACGAGTCTATAGCGGCGTTTGTATAAAAACGCC
ACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAACGCCACTAAAGTAGAGTCTTTAGCGGCA
TTTTTATAAAAACCCACTAAAGTATGAGTCTATA
Found at i:3758605 original size:40 final size:41
Alignment explanation
Indices: 3758151--3758665 Score: 432
Period size: 41 Copynumber: 12.5 Consensus size: 41
3758141 TTATAAACTT
* * * * *
3758151 GCGGCGTTTGTAAACACAAACGTCACTAAAGCACAAGTCTATA
1 GCGGCGTTTGTATA-A-AAACGCCACTAAAGTACGAGTCTTTA
* * * * **
3758194 GCGGTGTTTGTATAAGAACACCACTAAAGTATGAGTCGCTA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTA
* *
3758235 GCGGCATTTGTATAAAAGCGCCACTAAAGTACGAGTCTTTA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTA
* * * *
3758276 GTGACGTTTGTATAAAAAC-CCACTAAAGTATGAGTCTATA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTA
* * ** *
3758316 GTGGCGTTTGTAAACACAAATACCACTAAA-TCACGAGTCTATA
1 GCGGCGTTTGTATA-A-AAACGCCACTAAAGT-ACGAGTCTTTA
*
3758359 GCGACGTTTGTATAAAAACGCCACTAAAGGTACGAGTCTTTA
1 GCGGCGTTTGTATAAAAACGCCACTAAA-GTACGAGTCTTTA
* * * *
3758401 GTGGTGTTTGTATAAAAACGCCACTAAATTATGAGTCTTTA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTA
* * * *
3758442 GCGGCATTTTTATAAAAACACCAC-AAAGGTACTAG-CTTTTA
1 GCGGCGTTTGTATAAAAACGCCACTAAA-GTACGAGTC-TTTA
* * * * *
3758483 GCGGCGTTTGTATAAAAATGCCACTAAAATATGATTCTATA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTA
* * * **
3758524 GTGGCCTTTGTATAAAAATGCGTCTAAAGTAC-AGTCTTTA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTA
* *
3758564 GCGACGCTTT-TATAGAAACGCCACTAAAGTAC-AGTCTTTA
1 GCGGCG-TTTGTATAAAAACGCCACTAAAGTACGAGTCTTTA
* * * * * *
3758604 GCGGCATTTTTATAGAAACGCCGCTAAAATACTAGTCTTTA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTA
* *
3758645 GAGGCGTTTGTTCTAAAAACG
1 GCGGCGTTTG-TATAAAAACG
3758666 TTGCTAAAAA
Statistics
Matches: 378, Mismatches: 80, Indels: 29
0.78 0.16 0.06
Matches are distributed among these distances:
39 3 0.01
40 94 0.25
41 186 0.49
42 53 0.14
43 42 0.11
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (41 bp):
GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTA
Found at i:3770917 original size:29 final size:29
Alignment explanation
Indices: 3770791--3770918 Score: 114
Period size: 29 Copynumber: 4.4 Consensus size: 29
3770781 TATATTTGGA
* * * *
3770791 AATTATTGTATTTTGTAAAAGTATTGGGT
1 AATTATTGTAATTTATAAAAGTTTTGGGC
* * * *
3770820 AATAATCGTAAATTATAAAAGTTTTGGGT
1 AATTATTGTAATTTATAAAAGTTTTGGGC
* * * *
3770849 AA-TAATGTAAATTATAGAAGTTTTGAGC
1 AATTATTGTAATTTATAAAAGTTTTGGGC
** *
3770877 AATTATAATAATTTATAAAAGTTTTAGGC
1 AATTATTGTAATTTATAAAAGTTTTGGGC
3770906 AATTATTGTAATT
1 AATTATTGTAATT
3770919 GTAGTAGTTT
Statistics
Matches: 77, Mismatches: 21, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
28 22 0.29
29 55 0.71
ACGTcount: A:0.40, C:0.02, G:0.16, T:0.42
Consensus pattern (29 bp):
AATTATTGTAATTTATAAAAGTTTTGGGC
Found at i:3771913 original size:23 final size:23
Alignment explanation
Indices: 3771845--3771913 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
3771835 CAATCTTATA
*
3771845 TGGCACTACGGTGCATTTCTAAG
1 TGGCACTACGGTGCATTTCTACG
*
3771868 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCATTTCTACG
* * *
3771891 TGGGACTTCGGTGCATTTATACG
1 TGGCACTACGGTGCATTTCTACG
3771914 AGCTATGGTG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.20, C:0.22, G:0.28, T:0.30
Consensus pattern (23 bp):
TGGCACTACGGTGCATTTCTACG
Found at i:3772102 original size:28 final size:28
Alignment explanation
Indices: 3772049--3772102 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
3772039 TATGAATGGT
* * *
3772049 ATTATATGATTTATATGATGATATGTGG
1 ATTATATGATTTAAATGATCAAATGTGG
3772077 ATTATATGA-TTAAATGAGTCAAATGT
1 ATTATATGATTTAAATGA-TCAAATGT
3772103 TGGTTAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 7 0.32
28 15 0.68
ACGTcount: A:0.37, C:0.02, G:0.19, T:0.43
Consensus pattern (28 bp):
ATTATATGATTTAAATGATCAAATGTGG
Found at i:3777606 original size:29 final size:29
Alignment explanation
Indices: 3777479--3777642 Score: 130
Period size: 29 Copynumber: 5.7 Consensus size: 29
3777469 TATATTTGGA
* * *
3777479 AATTATTGTATTTTGTAAAAGTATTGGGT
1 AATTATTGTAATTTATAAAAGTTTTGGGT
* * *
3777508 AATAATCGTAAATTATAAAAGTTTTGGGT
1 AATTATTGTAATTTATAAAAGTTTTGGGT
* * * * * *
3777537 AATAAATGTAAATTATAGAAGTTTTGAGC
1 AATTATTGTAATTTATAAAAGTTTTGGGT
** * *
3777566 AATTATAATAATTTATAAAAGTTTTAGGC
1 AATTATTGTAATTTATAAAAGTTTTGGGT
* ** * *
3777595 AATTATTGTAATTTGTAGTAGTTTTTGTT
1 AATTATTGTAATTTATAAAAGTTTTGGGT
*
3777624 AATTTTTGTAATTTATAAA
1 AATTATTGTAATTTATAAA
3777643 GATCTTGGAT
Statistics
Matches: 104, Mismatches: 31, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
29 104 1.00
ACGTcount: A:0.38, C:0.02, G:0.15, T:0.45
Consensus pattern (29 bp):
AATTATTGTAATTTATAAAAGTTTTGGGT
Found at i:3780409 original size:65 final size:65
Alignment explanation
Indices: 3780334--3780490 Score: 203
Period size: 65 Copynumber: 2.4 Consensus size: 65
3780324 CACACCCATT
* *
3780334 TCGAATGCATTTTGTGTACCGATGCACA-AGCCATGCATCGATGCA-CTCATGAAT-ATTTTGAA
1 TCGAATGCATTTTGTGTACCGATGCACAGA-CCATGCATCGATGCACCCCAAG-ATCA-TTTGAA
3780396 ACA
63 ACA
* *
3780399 TCGAATGCATTTTGTGTACGGATGCACAGACCATGCATCGATGCACCCCAAGCTCATTTGAAACA
1 TCGAATGCATTTTGTGTACCGATGCACAGACCATGCATCGATGCACCCCAAGATCATTTGAAACA
* * *
3780464 TCGAATGTAATTAGTGTACCGATGCAC
1 TCGAATGCATTTTGTGTACCGATGCAC
3780491 CCATAGTGTA
Statistics
Matches: 81, Mismatches: 8, Indels: 6
0.85 0.08 0.06
Matches are distributed among these distances:
65 75 0.93
66 6 0.07
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (65 bp):
TCGAATGCATTTTGTGTACCGATGCACAGACCATGCATCGATGCACCCCAAGATCATTTGAAACA
Found at i:3786307 original size:23 final size:22
Alignment explanation
Indices: 3786277--3786357 Score: 92
Period size: 23 Copynumber: 3.6 Consensus size: 22
3786267 ACACTAGACA
3786277 GTGCATCGATGCATCCCTTGAAT
1 GTGCATCGATGCA-CCCTTGAAT
* * *
3786300 GTGCATCGATACA-CCATGAAG
1 GTGCATCGATGCACCCTTGAAT
* *
3786321 GTGCACCGATGCACTCCTTAAAT
1 GTGCATCGATGCAC-CCTTGAAT
3786344 GTGCATCGATGCAC
1 GTGCATCGATGCAC
3786358 TCTGTTGTTC
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
21 17 0.36
23 30 0.64
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (22 bp):
GTGCATCGATGCACCCTTGAAT
Found at i:3786324 original size:21 final size:20
Alignment explanation
Indices: 3786258--3786330 Score: 58
Period size: 21 Copynumber: 3.5 Consensus size: 20
3786248 TTGTGCACAA
*
3786258 TGCATCGATACACTA-GACAG
1 TGCATCGATACACCATGA-AG
* *
3786278 TGCATCGATGCATCCCTTGAATG
1 TGCATCGATACA--CCATGAA-G
3786301 TGCATCGATACACCATGAAGG
1 TGCATCGATACACCATGAA-G
*
3786322 TGCACCGAT
1 TGCATCGAT
3786331 GCACTCCTTA
Statistics
Matches: 42, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
20 11 0.26
21 15 0.36
22 2 0.05
23 14 0.33
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.23
Consensus pattern (20 bp):
TGCATCGATACACCATGAAG
Found at i:3786345 original size:44 final size:43
Alignment explanation
Indices: 3786258--3786353 Score: 124
Period size: 44 Copynumber: 2.2 Consensus size: 43
3786248 TTGTGCACAA
* * *
3786258 TGCATCGATACACTAGACAGTGCATCGATGCATCCCTTGAATG
1 TGCATCGATACACCAGACAGTGCACCGATGCATCCCTTAAATG
3786301 TGCATCGATACACCATGA-AGGTGCACCGATGCA-CTCCTTAAATG
1 TGCATCGATACACCA-GACA-GTGCACCGATGCATC-CCTTAAATG
3786345 TGCATCGAT
1 TGCATCGAT
3786354 GCACTCTGTT
Statistics
Matches: 47, Mismatches: 3, Indels: 5
0.85 0.05 0.09
Matches are distributed among these distances:
43 16 0.34
44 31 0.66
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.25
Consensus pattern (43 bp):
TGCATCGATACACCAGACAGTGCACCGATGCATCCCTTAAATG
Found at i:3788615 original size:65 final size:64
Alignment explanation
Indices: 3788490--3788646 Score: 167
Period size: 65 Copynumber: 2.4 Consensus size: 64
3788480 CACACCCATT
* *
3788490 TCGAATGCATTTTGTGTAACGTTGCACAAGCCATGCATCGATGCACTCGTGAATATTTTGAAACA
1 TCGAATGCATTTTGTGTAACGATGCACAAGCCATGCATCGATGCACTCG-CAATATTTTGAAACA
* * *
3788555 TTGAATGCATTTTGTGTACCGATGCA-TAGACCATGCATCGATGCACTC-CAAGCTCA-TTTGAA
1 TCGAATGCATTTTGTGTAACGATGCACAAG-CCATGCATCGATGCACTCGCAA--T-ATTTTGAA
3788617 ACA
62 ACA
* * * *
3788620 TCGAATGTAATTAGTGTATCGATGCAC
1 TCGAATGCATTTTGTGTAACGATGCAC
3788647 CCCTAGTGTA
Statistics
Matches: 77, Mismatches: 10, Indels: 9
0.80 0.10 0.09
Matches are distributed among these distances:
63 2 0.03
64 2 0.03
65 72 0.94
66 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (64 bp):
TCGAATGCATTTTGTGTAACGATGCACAAGCCATGCATCGATGCACTCGCAATATTTTGAAACA
Found at i:3791699 original size:64 final size:64
Alignment explanation
Indices: 3791627--3791753 Score: 254
Period size: 64 Copynumber: 2.0 Consensus size: 64
3791617 AATAAGTGTA
3791627 CACAAATGAGAAATCAACTTCTATAATTTTTTCTTTTATTTTTACTTAGCATCCAAACAATAAT
1 CACAAATGAGAAATCAACTTCTATAATTTTTTCTTTTATTTTTACTTAGCATCCAAACAATAAT
3791691 CACAAATGAGAAATCAACTTCTATAATTTTTTCTTTTATTTTTACTTAGCATCCAAACAATAA
1 CACAAATGAGAAATCAACTTCTATAATTTTTTCTTTTATTTTTACTTAGCATCCAAACAATAA
3791754 ATCATGCAGT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 63 1.00
ACGTcount: A:0.38, C:0.17, G:0.05, T:0.40
Consensus pattern (64 bp):
CACAAATGAGAAATCAACTTCTATAATTTTTTCTTTTATTTTTACTTAGCATCCAAACAATAAT
Found at i:3792649 original size:20 final size:20
Alignment explanation
Indices: 3792624--3792673 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
3792614 CGTGAGGAGC
3792624 AGATTTATCTCGCCGAGGCA
1 AGATTTATCTCGCCGAGGCA
**
3792644 AGATTTATCTCGTTGAGGCA
1 AGATTTATCTCGCCGAGGCA
3792664 AGATTTATCT
1 AGATTTATCT
3792674 AAAGAAGTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (20 bp):
AGATTTATCTCGCCGAGGCA
Found at i:3817596 original size:38 final size:38
Alignment explanation
Indices: 3817540--3817664 Score: 116
Period size: 38 Copynumber: 3.3 Consensus size: 38
3817530 GGTAATCCTT
* * *
3817540 ATGAAATAGTTTCTCTTAAAACAAAAGTTTTTTCTTAC
1 ATGAGATAGTTTTTCTTAAAACAAAAGTTTTTTCTCAC
*
3817578 ATGAGATAGTTTTTCTTAAAAC--AAGTTTTGTCTCAC
1 ATGAGATAGTTTTTCTTAAAACAAAAGTTTTTTCTCAC
* * *
3817614 -TAGAGACA-TTTTCTCTTAAAATAAAA-TTTTTATCTCGC
1 AT-GAGATAGTTTT-TCTTAAAACAAAAGTTTTT-TCTCAC
*
3817652 TTGAGATAGTTTT
1 ATGAGATAGTTTT
3817665 CTCTAGAAAA
Statistics
Matches: 71, Mismatches: 9, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
35 5 0.07
36 25 0.35
37 4 0.06
38 32 0.45
39 5 0.07
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.43
Consensus pattern (38 bp):
ATGAGATAGTTTTTCTTAAAACAAAAGTTTTTTCTCAC
Found at i:3817631 original size:36 final size:38
Alignment explanation
Indices: 3817549--3817668 Score: 104
Period size: 36 Copynumber: 3.2 Consensus size: 38
3817539 TATGAAATAG
* * *
3817549 TTTCTCTTAAAACAAAAGTTTTTTCTTACATGAGATAGT
1 TTTCTCTTAAAAC-AAAGTTTTGTCTCACATGAGACAGT
3817588 TTT-TCTTAAAAC-AAGTTTTGTCTCAC-TAGAGACA-T
1 TTTCTCTTAAAACAAAGTTTTGTCTCACAT-GAGACAGT
* * * * * *
3817623 TTTCTCTTAAAATAAAATTTTTATCTCGCTTGAGATAGT
1 TTTCTCTTAAAA-CAAAGTTTTGTCTCACATGAGACAGT
3817662 TTTCTCT
1 TTTCTCT
3817669 AGAAAATTTT
Statistics
Matches: 67, Mismatches: 8, Indels: 12
0.77 0.09 0.14
Matches are distributed among these distances:
35 5 0.07
36 25 0.37
38 25 0.37
39 12 0.18
ACGTcount: A:0.30, C:0.15, G:0.10, T:0.45
Consensus pattern (38 bp):
TTTCTCTTAAAACAAAGTTTTGTCTCACATGAGACAGT
Found at i:3817678 original size:35 final size:35
Alignment explanation
Indices: 3817636--3817887 Score: 196
Period size: 35 Copynumber: 7.2 Consensus size: 35
3817626 CTCTTAAAAT
* *
3817636 AAAATTTTTATCTCGCTTGAGATAGTTTTCTCTAG
1 AAAATTTTTATCTCACTTGAGATAGTTTTCTCTTG
** * *
3817671 AAAATTTTCGTCTCACTTGAGA-CGGTTTCTCTTG
1 AAAATTTTTATCTCACTTGAGATAGTTTTCTCTTG
* * *
3817705 AAATTTTTTTATTTCACTTGATATA-TTTTCTCTTG
1 AAA-ATTTTTATCTCACTTGAGATAGTTTTCTCTTG
* * *
3817740 AAGTAAATTTTATCTCACTCGAGAAAG-TTTCTCTTG
1 AA--AATTTTTATCTCACTTGAGATAGTTTTCTCTTG
* *
3817776 AAACAAAATTTTTATCTCCCTTGAGATAGTTTTCTGTTG
1 ----AAAATTTTTATCTCACTTGAGATAGTTTTCTCTTG
* * * *
3817815 AAAA--TTTGTCTCACTTGAGACA-ATTTCTC-TC
1 AAAATTTTTATCTCACTTGAGATAGTTTTCTCTTG
* *
3817846 AAAAATTTTCTCTCACTTGAGATA-TTTTCTCTTG
1 AAAATTTTTATCTCACTTGAGATAGTTTTCTCTTG
3817880 AATAATTT
1 AA-AATTT
3817888 CATCTTGTTA
Statistics
Matches: 168, Mismatches: 35, Indels: 28
0.73 0.15 0.12
Matches are distributed among these distances:
31 5 0.03
32 5 0.03
33 37 0.22
34 15 0.09
35 52 0.31
36 24 0.14
37 1 0.01
38 19 0.11
39 8 0.05
40 2 0.01
ACGTcount: A:0.27, C:0.16, G:0.12, T:0.45
Consensus pattern (35 bp):
AAAATTTTTATCTCACTTGAGATAGTTTTCTCTTG
Found at i:3817785 original size:144 final size:140
Alignment explanation
Indices: 3817603--3817881 Score: 369
Period size: 144 Copynumber: 2.0 Consensus size: 140
3817593 TTAAAACAAG
* * * * *
3817603 TTTTGTCTCACTAGAGACATTTTCTCTTAAAATAAAATTTTTATCTCGCTTGAGATAGTTTTCTC
1 TTTTATCTCACTAGAGAAAGTTTCTCTTAAAACAAAATTTTTATCTCCCTTGAGATAGTTTTCTC
** * ** * *
3817668 TAGAAAATTTTCGTCTCACTTGAGACGGTTTCTCTTGAAATTTTTTTATTTCACTTGATATATTT
66 TAGAAAA-TTT-GTCTCACTTGAGACAATTTCTC-TCAAA-AATTTTATCTCACTTGAGATATTT
3817733 TCTCTTGAAGTAAA
127 TCTCTTGAAGTAAA
* * *
3817747 TTTTATCTCACTCGAGAAAGTTTCTCTTGAAACAAAATTTTTATCTCCCTTGAGATAGTTTTCTG
1 TTTTATCTCACTAGAGAAAGTTTCTCTTAAAACAAAATTTTTATCTCCCTTGAGATAGTTTTCTC
* *
3817812 TTGAAAATTTGTCTCACTTGAGACAATTTCTCTCAAAAATTTTCTCTCACTTGAGATATTTTCTC
66 TAGAAAATTTGTCTCACTTGAGACAATTTCTCTCAAAAATTTTATCTCACTTGAGATATTTTCTC
3817877 TTGAA
131 TTGAA
3817882 TAATTTCATC
Statistics
Matches: 118, Mismatches: 17, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
140 28 0.24
141 4 0.03
142 20 0.17
143 3 0.03
144 63 0.53
ACGTcount: A:0.27, C:0.17, G:0.11, T:0.45
Consensus pattern (140 bp):
TTTTATCTCACTAGAGAAAGTTTCTCTTAAAACAAAATTTTTATCTCCCTTGAGATAGTTTTCTC
TAGAAAATTTGTCTCACTTGAGACAATTTCTCTCAAAAATTTTATCTCACTTGAGATATTTTCTC
TTGAAGTAAA
Found at i:3817827 original size:71 final size:72
Alignment explanation
Indices: 3817547--3817887 Score: 269
Period size: 74 Copynumber: 4.8 Consensus size: 72
3817537 CTTATGAAAT
* * *
3817547 AGTTTCTCTTAAAACAAAAGTTTTT-TCTTACATGAGATAGTTTT-TCTTAAAACAAGTTTTGTC
1 AGTTTCTCTTAAAACAAAA-TTTTTATCTCACTTGAGATAGTTTTCTC-TAGAA-AA-TTTTGTC
* *
3817610 TCACTAGAGAC
62 TCACTTGAGAA
* * *
3817621 ATTTTCTCTTAAAATAAAATTTTTATCTCGCTTGAGATAGTTTTCTCTAGAAAATTTTCGTCTCA
1 AGTTTCTCTTAAAACAAAATTTTTATCTCACTTGAGATAGTTTTCTCTAGAAAATTTT-GTCTCA
*
3817686 CTTGAGAC
65 CTTGAGAA
* * ** * * * *
3817694 GGTTTCTCTT--GA-AATTTTTTTATTTCACTTGATATA-TTTTCTCTTGAAGTAAATTTTATCT
1 AGTTTCTCTTAAAACAAAATTTTTATCTCACTTGAGATAGTTTTCTC-T--AGAAAATTTTGTCT
*
3817755 CACTCGAGAA
63 CACTTGAGAA
* * * *
3817765 AGTTTCTCTTGAAACAAAATTTTTATCTCCCTTGAGATAGTTTTCTGTTGAAAA-TTTGTCTCAC
1 AGTTTCTCTTAAAACAAAATTTTTATCTCACTTGAGATAGTTTTCTCTAGAAAATTTTGTCTCAC
3817829 TTGAGACA
66 TTGAGA-A
* * *
3817837 A-TTTCTC-T----CAAAAATTTTCTCTCACTTGAGATA-TTTTCTCTTGAATAATTT
1 AGTTTCTCTTAAAACAAAATTTTTATCTCACTTGAGATAGTTTTCTCTAGAA-AATTT
3817888 CATCTTGTTA
Statistics
Matches: 219, Mismatches: 35, Indels: 33
0.76 0.12 0.11
Matches are distributed among these distances:
65 11 0.05
66 24 0.11
67 2 0.01
69 7 0.03
70 21 0.10
71 41 0.19
72 19 0.09
73 29 0.13
74 57 0.26
75 8 0.04
ACGTcount: A:0.28, C:0.16, G:0.11, T:0.45
Consensus pattern (72 bp):
AGTTTCTCTTAAAACAAAATTTTTATCTCACTTGAGATAGTTTTCTCTAGAAAATTTTGTCTCAC
TTGAGAA
Found at i:3817834 original size:33 final size:32
Alignment explanation
Indices: 3817646--3817888 Score: 126
Period size: 33 Copynumber: 7.0 Consensus size: 32
3817636 AAAATTTTTA
* *
3817646 TCTCGCTTGAGATAGTTTTCTCTAGAAAATTTTC
1 TCTCACTTGAGATA-TTTTCTCTTGAAAA-TTTC
*** * *
3817680 GTCTCACTTGAGACGGTTTCTCTTGAAATTTTTTTA
1 -TCTCACTTGAGATATTTTCTCTTGAAA---ATTTC
* * *
3817716 TTTCACTTGATATATTTTCTCTTGAAGTAAATTTTA
1 TCTCACTTGAGATATTTTCTCTTG-A--AAA-TTTC
* * * *
3817752 TCTCACTCGAGAAAGTTTCTCTTGAAACAAAATTTTTA
1 TCTCACTTGAGATATTTTCTCTTG----AAAA--TTTC
* * *
3817790 TCTCCCTTGAGATAGTTTTCTGTTGAAAATTTG
1 TCTCACTTGAGATA-TTTTCTCTTGAAAATTTC
* * **
3817823 TCTCACTTGAGACAATTTCTCTCAAAAATTTTC
1 TCTCACTTGAGATATTTTCTCTTGAAAA-TTTC
3817856 TCTCACTTGAGATATTTTCTCTTGAATAATTTC
1 TCTCACTTGAGATATTTTCTCTTGAA-AATTTC
3817889 ATCTTGTTAG
Statistics
Matches: 158, Mismatches: 36, Indels: 30
0.71 0.16 0.13
Matches are distributed among these distances:
32 10 0.06
33 44 0.28
34 13 0.08
35 34 0.22
36 27 0.17
37 3 0.02
38 18 0.11
39 9 0.06
ACGTcount: A:0.26, C:0.17, G:0.12, T:0.45
Consensus pattern (32 bp):
TCTCACTTGAGATATTTTCTCTTGAAAATTTC
Found at i:3818171 original size:22 final size:22
Alignment explanation
Indices: 3818143--3818240 Score: 111
Period size: 22 Copynumber: 4.8 Consensus size: 22
3818133 AATACTAAGA
3818143 GGTACCGATACCCCTATGAATG
1 GGTACCGATACCCCTATGAATG
3818165 GGTACCGATACCCCTATGAATG
1 GGTACCGATACCCCTATGAATG
*
3818187 GGTACCGACA-CCC------TG
1 GGTACCGATACCCCTATGAATG
*
3818202 GGTACCGATACCCCTATGACTG
1 GGTACCGATACCCCTATGAATG
* *
3818224 GGTATCAATACCCCTAT
1 GGTACCGATACCCCTAT
3818241 AACTGCTCAA
Statistics
Matches: 65, Mismatches: 4, Indels: 14
0.78 0.05 0.17
Matches are distributed among these distances:
15 11 0.17
16 3 0.05
21 3 0.05
22 48 0.74
ACGTcount: A:0.26, C:0.31, G:0.21, T:0.22
Consensus pattern (22 bp):
GGTACCGATACCCCTATGAATG
Found at i:3818205 original size:15 final size:15
Alignment explanation
Indices: 3818185--3818214 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3818175 CCCCTATGAA
3818185 TGGGTACCGACACCC
1 TGGGTACCGACACCC
*
3818200 TGGGTACCGATACCC
1 TGGGTACCGACACCC
3818215 CTATGACTGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.37, G:0.27, T:0.17
Consensus pattern (15 bp):
TGGGTACCGACACCC
Found at i:3818245 original size:22 final size:22
Alignment explanation
Indices: 3818199--3818245 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
3818189 TACCGACACC
* *
3818199 CTGGGTACCGATACCCCTATGA
1 CTGGGTACCAATACCCCTATAA
*
3818221 CTGGGTATCAATACCCCTATAA
1 CTGGGTACCAATACCCCTATAA
3818243 CTG
1 CTG
3818246 CTCAAACATC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.26, C:0.30, G:0.19, T:0.26
Consensus pattern (22 bp):
CTGGGTACCAATACCCCTATAA
Found at i:3821557 original size:18 final size:19
Alignment explanation
Indices: 3821527--3821578 Score: 72
Period size: 18 Copynumber: 2.8 Consensus size: 19
3821517 GAACCAGTTT
*
3821527 AACTCGTTAACTTTGATCG
1 AACTCGTTGACTTTGATCG
*
3821546 AAC-CGTTGACTTTGATTG
1 AACTCGTTGACTTTGATCG
3821564 AACTC-TTGACTTTGA
1 AACTCGTTGACTTTGA
3821579 CCCATCCATT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
18 26 0.87
19 4 0.13
ACGTcount: A:0.25, C:0.19, G:0.17, T:0.38
Consensus pattern (19 bp):
AACTCGTTGACTTTGATCG
Found at i:3826323 original size:19 final size:19
Alignment explanation
Indices: 3826299--3826336 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
3826289 TTGTTTTTAC
3826299 CTTTTAGTATTTATGTTAT
1 CTTTTAGTATTTATGTTAT
3826318 CTTTTAGTATTTATGTTAT
1 CTTTTAGTATTTATGTTAT
3826337 ATATGGTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.05, G:0.11, T:0.63
Consensus pattern (19 bp):
CTTTTAGTATTTATGTTAT
Found at i:3835537 original size:19 final size:20
Alignment explanation
Indices: 3835498--3835538 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
3835488 AAAATCTTTC
* *
3835498 ATTTTGTTTTTCAAAATCAA
1 ATTTTGCTTTTCAAAACCAA
3835518 ATTTTGCTTTT-AAAACCAA
1 ATTTTGCTTTTCAAAACCAA
3835537 AT
1 AT
3835539 CATTTTCATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.37, C:0.12, G:0.05, T:0.46
Consensus pattern (20 bp):
ATTTTGCTTTTCAAAACCAA
Found at i:3836008 original size:17 final size:18
Alignment explanation
Indices: 3835983--3836018 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
3835973 CTCACCTCCT
*
3835983 TCTTTTTATT-ATTCTTC
1 TCTTGTTATTCATTCTTC
3836000 TCTTGTTATTCATTCTTC
1 TCTTGTTATTCATTCTTC
3836018 T
1 T
3836019 TTTTTAGTAT
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:0.11, C:0.19, G:0.03, T:0.67
Consensus pattern (18 bp):
TCTTGTTATTCATTCTTC
Found at i:3838552 original size:21 final size:21
Alignment explanation
Indices: 3838527--3838599 Score: 110
Period size: 21 Copynumber: 3.5 Consensus size: 21
3838517 ATTTCTCCTG
* *
3838527 AAGGACCACATATATGTCCCG
1 AAGGACCACTTATATGTCCCA
3838548 AAGGACCACTTATATGTCCCA
1 AAGGACCACTTATATGTCCCA
*
3838569 AAGAACCACTTATATGTCCCA
1 AAGGACCACTTATATGTCCCA
*
3838590 AAGCACCACT
1 AAGGACCACT
3838600 CCTTAAGGAT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 48 1.00
ACGTcount: A:0.36, C:0.30, G:0.14, T:0.21
Consensus pattern (21 bp):
AAGGACCACTTATATGTCCCA
Found at i:3838616 original size:77 final size:77
Alignment explanation
Indices: 3838521--3838669 Score: 190
Period size: 77 Copynumber: 1.9 Consensus size: 77
3838511 CATAGAATTT
* * ** *
3838521 CTCCTGAAGGACCACATATATGTCCCGAAGGACCACTTATATGTCCCAAAGAACCACTTATATGT
1 CTCCTGAAGGACCACATATATATCCCAAAGGACCAAATATATGTCCCAAAGAACCACATATATGT
3838586 CCCAAAGCACCA
66 CCCAAAGCACCA
* * * * * *
3838598 CTCCTTAAGGATCACATATATATTCCAAAGGACCAAATATGTGTCCCGATGAACCACATATATGT
1 CTCCTGAAGGACCACATATATATCCCAAAGGACCAAATATATGTCCCAAAGAACCACATATATGT
*
3838663 TCCAAAG
66 CCCAAAG
3838670 GATTATATAT
Statistics
Matches: 60, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
77 60 1.00
ACGTcount: A:0.35, C:0.28, G:0.14, T:0.23
Consensus pattern (77 bp):
CTCCTGAAGGACCACATATATATCCCAAAGGACCAAATATATGTCCCAAAGAACCACATATATGT
CCCAAAGCACCA
Found at i:3838680 original size:42 final size:42
Alignment explanation
Indices: 3838610--3838699 Score: 108
Period size: 42 Copynumber: 2.1 Consensus size: 42
3838600 CCTTAAGGAT
* *
3838610 CACATATATATTCCAAAGGACCAAATATGTGTCCCGATGAAC
1 CACATATATATTCCAAAGGACCAAATATGTATCCCGAAGAAC
* ** * * *
3838652 CACATATATGTTCCAAAGGATTATATATGTATCCTGAAGGAC
1 CACATATATATTCCAAAGGACCAAATATGTATCCCGAAGAAC
3838694 CACATA
1 CACATA
3838700 GAACCCTCGA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.27
Consensus pattern (42 bp):
CACATATATATTCCAAAGGACCAAATATGTATCCCGAAGAAC
Found at i:3839970 original size:20 final size:20
Alignment explanation
Indices: 3839931--3839971 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
3839921 ATTAATTTAA
* *
3839931 TCTTAATTTTTAAATTTTAT
1 TCTTAAATTTTAAATATTAT
*
3839951 TCTTAAATTTTACATATTAT
1 TCTTAAATTTTAAATATTAT
3839971 T
1 T
3839972 TCAATTAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (20 bp):
TCTTAAATTTTAAATATTAT
Found at i:3843629 original size:23 final size:23
Alignment explanation
Indices: 3843602--3843668 Score: 89
Period size: 23 Copynumber: 2.9 Consensus size: 23
3843592 ATTTTATATA
3843602 GCACTTCGGTGCATTTCTACGCG
1 GCACTTCGGTGCATTTCTACGCG
* * *
3843625 GCACTACGGTGCAATTCTACGTG
1 GCACTTCGGTGCATTTCTACGCG
* *
3843648 TCACTTCGGTGCATTTATACG
1 GCACTTCGGTGCATTTCTACG
3843669 AGTTGTGGTG
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.18, C:0.27, G:0.24, T:0.31
Consensus pattern (23 bp):
GCACTTCGGTGCATTTCTACGCG
Found at i:3843719 original size:16 final size:17
Alignment explanation
Indices: 3843698--3843731 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
3843688 GTGCACAACC
3843698 TCTATAG-ACTCACATA
1 TCTATAGTACTCACATA
*
3843714 TCTATAGTTCTCACATA
1 TCTATAGTACTCACATA
3843731 T
1 T
3843732 GTACATGGGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.32, C:0.24, G:0.06, T:0.38
Consensus pattern (17 bp):
TCTATAGTACTCACATA
Found at i:3844487 original size:16 final size:17
Alignment explanation
Indices: 3844455--3844488 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
3844445 ATTTATTATA
3844455 TTTTGACAAAGTAAATG
1 TTTTGACAAAGTAAATG
*
3844472 TTTTGA-AAAGTTAATG
1 TTTTGACAAAGTAAATG
3844488 T
1 T
3844489 GACATCTCGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.38, C:0.03, G:0.18, T:0.41
Consensus pattern (17 bp):
TTTTGACAAAGTAAATG
Found at i:3848662 original size:29 final size:29
Alignment explanation
Indices: 3848602--3848763 Score: 236
Period size: 29 Copynumber: 5.6 Consensus size: 29
3848592 CACATTTGAA
3848602 AATTCCCAAAATGTCACC-TTTTCAAAAT
1 AATTCCCAAAATGTCACCTTTTTCAAAAT
* *
3848630 AATTCACAAAATATCACCTTTTTCAAAAT
1 AATTCCCAAAATGTCACCTTTTTCAAAAT
*
3848659 AATTCCCAAAGTGTCACCTTTTTCAAAAT
1 AATTCCCAAAATGTCACCTTTTTCAAAAT
* * *
3848688 AATTCCCAAAGTGTGACTTTTTTCAAAAT
1 AATTCCCAAAATGTCACCTTTTTCAAAAT
* * *
3848717 AAATCCCAGAATATCACCTTTTTCAAAAT
1 AATTCCCAAAATGTCACCTTTTTCAAAAT
3848746 AATTCCCAAAATGTCACC
1 AATTCCCAAAATGTCACC
3848764 GGGTCCGGTC
Statistics
Matches: 117, Mismatches: 16, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
28 16 0.14
29 101 0.86
ACGTcount: A:0.39, C:0.23, G:0.05, T:0.33
Consensus pattern (29 bp):
AATTCCCAAAATGTCACCTTTTTCAAAAT
Found at i:3855711 original size:29 final size:29
Alignment explanation
Indices: 3855666--3855763 Score: 153
Period size: 29 Copynumber: 3.4 Consensus size: 29
3855656 CGAACAAAAT
*
3855666 CAAAATGTCACATTTTTCAAAATAATTCC
1 CAAAATGTCACCTTTTTCAAAATAATTCC
*
3855695 CAGAATGTCACCTTTTTCAAAATAATTCC
1 CAAAATGTCACCTTTTTCAAAATAATTCC
*
3855724 CAAAATGTCA-CATTTTCAAAATAATTCC
1 CAAAATGTCACCTTTTTCAAAATAATTCC
*
3855752 AAAAATGTCACC
1 CAAAATGTCACC
3855764 GGAACTTTGA
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
28 26 0.41
29 37 0.59
ACGTcount: A:0.41, C:0.22, G:0.05, T:0.32
Consensus pattern (29 bp):
CAAAATGTCACCTTTTTCAAAATAATTCC
Found at i:3860319 original size:257 final size:258
Alignment explanation
Indices: 3860014--3860530 Score: 1018
Period size: 257 Copynumber: 2.0 Consensus size: 258
3860004 GAAATAATTA
3860014 AAATATTGACATTTTTAAGATTTTAGAAAATTAGGGAAGAAGATACACTATTATTTATTTCTAAT
1 AAATATTGACATTTTTAAGATTTTAGAAAATTAGGGAAGAAGATACACTATTATTTATTTCTAAT
3860079 TAAAGAAAAAATTAACTCCATAGTTTCATTAAGAAAAGATGTGCAATTTAATCGCATTGATAAGA
66 TAAAGAAAAAATTAACTCCATAGTTTCATTAAGAAAAGATGTGCAATTTAATCGCATTGATAAGA
*
3860144 GCCAAGAAAGCTTCGAGATACTAAAGGAAATATTAATGGAAATCCCAGTGCTAGTGCATCC-AAA
131 GCCAAGAAAGCTTCGAGATACTAAAGAAAATATTAATGGAAATCCCAGTGCTAGTGCATCCAAAA
3860208 TTTGTAAAATATTATGCAATTTATATTGATACATCTCATAATGGTTTTATTGTGTATTGCTGT
196 TTTGTAAAATATTATGCAATTTATATTGATACATCTCATAATGGTTTTATTGTGTATTGCTGT
3860271 AAATATTGACATTTTTAAGATTTTAGAAAATTAGGGAAGAAGATACACTATTATTTATTTCTAAT
1 AAATATTGACATTTTTAAGATTTTAGAAAATTAGGGAAGAAGATACACTATTATTTATTTCTAAT
3860336 TAAAGAAAAAATTAACTCCATAGTTTCATTAAGAAAAGATGTGCAATTTAATCGCATTGATAAGA
66 TAAAGAAAAAATTAACTCCATAGTTTCATTAAGAAAAGATGTGCAATTTAATCGCATTGATAAGA
3860401 GCCAAGAAAGCTTCGAGATACTAAAGAAAATATTAATGGAAATCCCAGTGCTAGTGCATCCAAAA
131 GCCAAGAAAGCTTCGAGATACTAAAGAAAATATTAATGGAAATCCCAGTGCTAGTGCATCCAAAA
3860466 TTTGTAAAATATTATGCAATTTATATTGATACATCTCATAATGGTTTTATTGTGTATTGCTGT
196 TTTGTAAAATATTATGCAATTTATATTGATACATCTCATAATGGTTTTATTGTGTATTGCTGT
3860529 AA
1 AA
3860531 GAAGAAAAAT
Statistics
Matches: 258, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
257 190 0.74
258 68 0.26
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.34
Consensus pattern (258 bp):
AAATATTGACATTTTTAAGATTTTAGAAAATTAGGGAAGAAGATACACTATTATTTATTTCTAAT
TAAAGAAAAAATTAACTCCATAGTTTCATTAAGAAAAGATGTGCAATTTAATCGCATTGATAAGA
GCCAAGAAAGCTTCGAGATACTAAAGAAAATATTAATGGAAATCCCAGTGCTAGTGCATCCAAAA
TTTGTAAAATATTATGCAATTTATATTGATACATCTCATAATGGTTTTATTGTGTATTGCTGT
Found at i:3862035 original size:150 final size:151
Alignment explanation
Indices: 3861764--3862064 Score: 579
Period size: 150 Copynumber: 2.0 Consensus size: 151
3861754 GAGCTTAAGG
3861764 ATTGAAATATCATCATATATGACCTAATTAAGGAAAATAAAGAAAAATTAAAGAATATTCAAGAT
1 ATTGAAATATCATCATATATGACCTAATTAAGGAAAATAAAGAAAAATTAAAGAATATTCAAGAT
3861829 AATCTTAAGACTAATTTTGATCAAAAAAAGTCTTATTCGAACATGAAGAGAAAT-AAATTGTA-T
66 AATCTTAAGACTAATTTTGATCAAAAAAAGTCTTATTCGAACATGAAGAGAAATAAAATTG-AGT
3861892 ATCAAGTTGGTGATAAAGTATT
130 ATCAAGTTGGTGATAAAGTATT
3861914 ATTGAAATATCATCATATATGACCTAATTAAGGAAAATAAAGAAAAATTAAAGAATATTCAAGAT
1 ATTGAAATATCATCATATATGACCTAATTAAGGAAAATAAAGAAAAATTAAAGAATATTCAAGAT
3861979 AATCTTAAGACTAATTTTGATCAAAAAAAGTCTTATTCGAACATGAAGAGAAATAAAATTGAGTA
66 AATCTTAAGACTAATTTTGATCAAAAAAAGTCTTATTCGAACATGAAGAGAAATAAAATTGAGTA
3862044 TCAAGTTGGTGATAAAGTATT
131 TCAAGTTGGTGATAAAGTATT
3862065 TCTTATAGTA
Statistics
Matches: 149, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
150 120 0.81
151 29 0.19
ACGTcount: A:0.48, C:0.08, G:0.14, T:0.30
Consensus pattern (151 bp):
ATTGAAATATCATCATATATGACCTAATTAAGGAAAATAAAGAAAAATTAAAGAATATTCAAGAT
AATCTTAAGACTAATTTTGATCAAAAAAAGTCTTATTCGAACATGAAGAGAAATAAAATTGAGTA
TCAAGTTGGTGATAAAGTATT
Found at i:3864619 original size:18 final size:18
Alignment explanation
Indices: 3864596--3864649 Score: 108
Period size: 18 Copynumber: 3.0 Consensus size: 18
3864586 GCCAAATTTG
3864596 GTATCGATACTTAAGAAA
1 GTATCGATACTTAAGAAA
3864614 GTATCGATACTTAAGAAA
1 GTATCGATACTTAAGAAA
3864632 GTATCGATACTTAAGAAA
1 GTATCGATACTTAAGAAA
3864650 TAGTATCAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.44, C:0.11, G:0.17, T:0.28
Consensus pattern (18 bp):
GTATCGATACTTAAGAAA
Found at i:3871114 original size:20 final size:20
Alignment explanation
Indices: 3871089--3871139 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
3871079 AATAAGTCAG
3871089 TAGTATCGATACCCAGAGGT
1 TAGTATCGATACCCAGAGGT
*
3871109 TAGTATCGATACCCATAGGT
1 TAGTATCGATACCCAGAGGT
*
3871129 TAATATCGATA
1 TAGTATCGATA
3871140 ATGAGTAGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (20 bp):
TAGTATCGATACCCAGAGGT
Found at i:3882813 original size:42 final size:42
Alignment explanation
Indices: 3882750--3882860 Score: 168
Period size: 42 Copynumber: 2.6 Consensus size: 42
3882740 TATTATAAAG
* *
3882750 CTTTAATTGTTAAAGTCCATGGCTTTGTCTTATTCCATAGTA
1 CTTTAATTATTAAATTCCATGGCTTTGTCTTATTCCATAGTA
* * *
3882792 CTTTAATTATTAAATTTCATGGCTTTTTCTTATTCCATAGTG
1 CTTTAATTATTAAATTCCATGGCTTTGTCTTATTCCATAGTA
*
3882834 CTTTAATTATTAAATTCCATTGCTTTG
1 CTTTAATTATTAAATTCCATGGCTTTG
3882861 CCTTCTCCCT
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 61 1.00
ACGTcount: A:0.24, C:0.15, G:0.11, T:0.50
Consensus pattern (42 bp):
CTTTAATTATTAAATTCCATGGCTTTGTCTTATTCCATAGTA
Found at i:3883855 original size:23 final size:22
Alignment explanation
Indices: 3883829--3883904 Score: 66
Period size: 23 Copynumber: 3.4 Consensus size: 22
3883819 AGTAAGTAAA
*
3883829 AAAAACAAATAATAAAATATAAT
1 AAAAACAAA-AACAAAATATAAT
* *
3883852 AAAAAAGAAAAAGAAAATA-AAT
1 -AAAAACAAAAACAAAATATAAT
3883874 AAATAAACAAAAACAAAA-ATAAT
1 -AA-AAACAAAAACAAAATATAAT
*
3883897 AATAACAA
1 AAAAACAA
3883905 GTACGAATAA
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
21 5 0.11
22 9 0.20
23 23 0.51
24 8 0.18
ACGTcount: A:0.78, C:0.05, G:0.03, T:0.14
Consensus pattern (22 bp):
AAAAACAAAAACAAAATATAAT
Found at i:3884442 original size:22 final size:22
Alignment explanation
Indices: 3884417--3884531 Score: 78
Period size: 22 Copynumber: 5.3 Consensus size: 22
3884407 ATATATAACA
3884417 AATAAATAATATAAAATAATAC
1 AATAAATAATATAAAATAATAC
* *
3884439 AAT-AATAATACAAGAATAATAA
1 AATAAATAATATAA-AATAATAC
* * * *
3884461 AAGAAAGAA-AGTAAAAAAATAT
1 AATAAATAATA-TAAAATAATAC
*
3884483 AATAATAAAATATAAAA-AATAC
1 AATAA-ATAATATAAAATAATAC
* *
3884505 -ATATATAATAT-AAATAAGTAG
1 AATAAATAATATAAAATAA-TAC
3884526 AATAAA
1 AATAAA
3884532 GGAAATATAT
Statistics
Matches: 71, Mismatches: 14, Indels: 16
0.70 0.14 0.16
Matches are distributed among these distances:
19 3 0.04
20 8 0.11
21 14 0.20
22 31 0.44
23 14 0.20
24 1 0.01
ACGTcount: A:0.69, C:0.03, G:0.05, T:0.23
Consensus pattern (22 bp):
AATAAATAATATAAAATAATAC
Found at i:3884464 original size:11 final size:11
Alignment explanation
Indices: 3884421--3884465 Score: 56
Period size: 11 Copynumber: 4.2 Consensus size: 11
3884411 ATAACAAATA
*
3884421 AATAATATAA-
1 AATAATACAAG
*
3884431 AATAATACAAT
1 AATAATACAAG
3884442 AATAATACAAG
1 AATAATACAAG
*
3884453 AATAATAAAAG
1 AATAATACAAG
3884464 AA
1 AA
3884466 AGAAAGTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
10 9 0.29
11 22 0.71
ACGTcount: A:0.69, C:0.04, G:0.04, T:0.22
Consensus pattern (11 bp):
AATAATACAAG
Found at i:3884515 original size:33 final size:33
Alignment explanation
Indices: 3884478--3884563 Score: 81
Period size: 33 Copynumber: 2.6 Consensus size: 33
3884468 AAAGTAAAAA
3884478 AATATAATAATAAAATATAA-AAAATACATATA-T
1 AATATAATAATAAAATATAAGAAAAT--ATATAGT
* *
3884511 AATATAAATAAGTAGAATA-AAGGAAATATATAGT
1 AATAT-AATAA-TAAAATATAAGAAAATATATAGT
*
3884545 AAAATAATAAT-AAATATAA
1 AATATAATAATAAAATATAA
3884564 TAGTAATAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
31 4 0.09
32 3 0.07
33 15 0.34
34 12 0.27
35 10 0.23
ACGTcount: A:0.65, C:0.01, G:0.06, T:0.28
Consensus pattern (33 bp):
AATATAATAATAAAATATAAGAAAATATATAGT
Found at i:3884550 original size:21 final size:22
Alignment explanation
Indices: 3884511--3884577 Score: 64
Period size: 24 Copynumber: 2.9 Consensus size: 22
3884501 ATACATATAT
* *
3884511 AATATAAATAAGTAGAATAAAGGA
1 AATAT-AAT-AGTAAAATAAAAGA
*
3884535 AATAT-ATAGTAAAATAATAATA
1 AATATAATAGTAAAATAA-AAGA
3884557 AATATAATAGTAATAATAAAA
1 AATATAATAGTAA-AATAAAA
3884578 ATGCAAAGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
21 9 0.24
22 9 0.24
23 9 0.24
24 10 0.27
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.27
Consensus pattern (22 bp):
AATATAATAGTAAAATAAAAGA
Found at i:3884565 original size:9 final size:10
Alignment explanation
Indices: 3884417--3884576 Score: 52
Period size: 11 Copynumber: 15.6 Consensus size: 10
3884407 ATATATAACA
3884417 AATAAATAAT
1 AATAAATAAT
3884427 -AT-AA-AAT
1 AATAAATAAT
3884434 AATACAATAAT
1 AATA-AATAAT
*
3884445 AATACAAGAAT
1 AATA-AATAAT
3884456 AATAAA-AGA-
1 AATAAATA-AT
*
3884465 AAGAAAGTAA-
1 AATAAA-TAAT
*
3884475 AAAAATATAAT
1 AATAA-ATAAT
3884486 AATAAA-ATAT
1 AATAAATA-AT
*
3884496 AAAAAATACAT
1 AATAAATA-AT
3884507 ATATAATATAAAT
1 A-ATAA-AT-AAT
3884520 AAGTAGAATAA-
1 AA-TA-AATAAT
**
3884531 AGGAAATATAT
1 AATAAATA-AT
*
3884542 AGTAAAATAAT
1 AAT-AAATAAT
3884553 AATAAAT-AT
1 AATAAATAAT
*
3884562 AAT-AGTAAT
1 AATAAATAAT
3884571 AATAAA
1 AATAAA
3884577 AATGCAAAGA
Statistics
Matches: 116, Mismatches: 13, Indels: 42
0.68 0.08 0.25
Matches are distributed among these distances:
7 3 0.03
8 6 0.05
9 23 0.20
10 28 0.24
11 34 0.29
12 11 0.09
13 9 0.08
14 2 0.02
ACGTcount: A:0.67, C:0.02, G:0.06, T:0.25
Consensus pattern (10 bp):
AATAAATAAT
Found at i:3884579 original size:20 final size:20
Alignment explanation
Indices: 3884475--3884579 Score: 62
Period size: 20 Copynumber: 5.3 Consensus size: 20
3884465 AAGAAAGTAA
*
3884475 AAAAATATAATAATAA-AAT
1 AAAAATATAATAGTAATAAT
*
3884494 ATAAAAAATACATA-T-ATAAT
1 A-AAAATATA-ATAGTAATAAT
* *
3884514 ATAAATA-AGTAG-AATAA-
1 AAAAATATAATAGTAATAAT
*
3884531 AGGAAATAT-ATAGTAAAATAAT
1 A-AAAATATAATAGT--AATAAT
3884553 AATAAATATAATAGTAATAAT
1 AA-AAATATAATAGTAATAAT
3884574 AAAAAT
1 AAAAAT
3884580 GCAAAGAAAA
Statistics
Matches: 66, Mismatches: 7, Indels: 25
0.67 0.07 0.26
Matches are distributed among these distances:
17 3 0.05
18 13 0.20
19 6 0.09
20 16 0.24
21 16 0.24
22 7 0.11
23 5 0.08
ACGTcount: A:0.66, C:0.01, G:0.06, T:0.28
Consensus pattern (20 bp):
AAAAATATAATAGTAATAAT
Found at i:3885154 original size:37 final size:37
Alignment explanation
Indices: 3885113--3885217 Score: 147
Period size: 37 Copynumber: 2.8 Consensus size: 37
3885103 GTGCTTGTGG
** *
3885113 ATCCTATCATTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTAAATCCTAGTAGAACTCT
* * *
3885150 ATCCTATTTTTAGGAGTTTAAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTAAATCCTAGTAGAACTCT
*
3885187 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTAAATCCTAGTAG
3885218 GACAAAAAGG
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.39
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTAAATCCTAGTAGAACTCT
Found at i:3886272 original size:106 final size:106
Alignment explanation
Indices: 3885940--3886451 Score: 624
Period size: 106 Copynumber: 4.9 Consensus size: 106
3885930 AGCATTGTTC
* * * * **
3885940 TGAGTCCAATATCCTCCGTTGTGAAGTAGAAATTGGCTCTGGAACCGAGAAATTGTTTGTTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACA
* * **
3886005 ACCAGCTGTCCCTTCGTTGTGAAGTTGAACTTTTGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
** **
3886046 CAAGTCCAATATCCTTCGCTGTGAAGTTGAAATTAACTCTG-AA-T--GAAA-T-TTTGTTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACA
** * * * *
3886105 ATTAGCCG-CCTCTTCGTCGTGAAGTTGAGCTTGTGTTGCCT
66 ACCAGCGGTCC-CTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* ** * * * * * *
3886146 TGGGTTAAAGATCATTCGCTGAGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACA
3886211 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * *
3886252 TGAGTCCAATATCCTACGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACA
3886317 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * * * *
3886358 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGATAAGTTGTTTGTTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACA
*
3886423 ACCAGCGGTCCCTTCGTCATGAAGTTGAA
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAA
3886452 ATTGGCTCTG
Statistics
Matches: 348, Mismatches: 50, Indels: 16
0.84 0.12 0.04
Matches are distributed among these distances:
99 2 0.01
100 72 0.21
101 3 0.01
102 5 0.01
104 3 0.01
105 3 0.01
106 258 0.74
107 2 0.01
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (106 bp):
TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACA
ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
Found at i:3886433 original size:212 final size:207
Alignment explanation
Indices: 3885941--3886451 Score: 641
Period size: 206 Copynumber: 2.4 Consensus size: 207
3885931 GCATTGTTCT
* * * ** *
3885941 GAGTCCAATATCCTCCGTTGTGAAGTAGAAATTGGCTCTGGAACCGAGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
* * ** *
3886006 CCAGCTGTCCCTTCGTTGTGAAGTTGAACTTTTGTTGTCTCAAGTCCAATATCCTTCGCTGTGAA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCAAGTCCAATATCCTACGCTGTGAA
* ** *
3886071 GTTGAAATTAACTCTGAATGAAATTTTGTTGACAATTAGCCGCCTCTTCGTCGTGAAGTTGAGCT
131 GTTGAAATTAACTCTGAATGAAATTTTATTGACAACCAGCCGCCTCTTCGTCGTGAAGTTGAACT
*
3886136 TGTGTTGCCTTG
196 TGCGTTGCCTTG
** * * * * * *
3886148 G-GTTAAAGATCATTCGCTGAGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
**
3886212 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCCTACGCTGTGAA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCAAGTCCAATATCCTACGCTGTGAA
** *
3886277 GTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCC-CTTCGTCGTGAAG
131 GTTGAAATTAACTCTG-AA-T--GAAA-T-TTTATTGACAACCAGCCG-CCTCTTCGTCGTGAAG
*
3886341 TTGAACTTGCGTTGTC-TG
189 TTGAACTTGCGTTGCCTTG
* *
3886359 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGATAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
*
3886424 CCAGCGGTCCCTTCGTCATGAAGTTGAA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAA
3886452 ATTGGCTCTG
Statistics
Matches: 255, Mismatches: 41, Indels: 11
0.83 0.13 0.04
Matches are distributed among these distances:
206 121 0.47
207 3 0.01
208 1 0.00
210 4 0.02
211 4 0.02
212 120 0.47
213 2 0.01
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (207 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCAAGTCCAATATCCTACGCTGTGAA
GTTGAAATTAACTCTGAATGAAATTTTATTGACAACCAGCCGCCTCTTCGTCGTGAAGTTGAACT
TGCGTTGCCTTG
Found at i:3886450 original size:63 final size:63
Alignment explanation
Indices: 3886370--3886514 Score: 229
Period size: 63 Copynumber: 2.3 Consensus size: 63
3886360 AGTCCAATAT
* * *
3886370 CCTTCGTTGTGAAGTTGAAATTGGCTCT-AAAATTGATAAGTTGTTTGTTGACAACCAGCGGTC
1 CCTTCGTCGTGAAGTTGAAATTGGCTCTGAAAATTG-GAAGTTGTTTATTGACAACCAGCGGTC
* *
3886433 CCTTCGTCATGAAGTTGAAATTGGCTCTGAAATTTGGAAGTTGTTTATTGACAACCAGCGGTC
1 CCTTCGTCGTGAAGTTGAAATTGGCTCTGAAAATTGGAAGTTGTTTATTGACAACCAGCGGTC
3886496 CCTTCGTCGTGAAGTTGAA
1 CCTTCGTCGTGAAGTTGAA
3886515 CTTGCGTTGT
Statistics
Matches: 75, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
63 69 0.92
64 6 0.08
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (63 bp):
CCTTCGTCGTGAAGTTGAAATTGGCTCTGAAAATTGGAAGTTGTTTATTGACAACCAGCGGTC
Found at i:3886484 original size:169 final size:166
Alignment explanation
Indices: 3886273--3886617 Score: 582
Period size: 169 Copynumber: 2.1 Consensus size: 166
3886263 TCCTACGCTG
3886273 TGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTG
1 TGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTG
*
3886338 AAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAAT
66 AAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAAT
* *
3886403 TGATAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTC
131 TGAGAAATTGTTTGTTGACAACCA-C-GTCCCTTCGTC
* *
3886441 ATGAAGTTGAAATTGGCTCTGAAATTTGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGT
1 -TGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGT
* *
3886506 GAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAA
65 GAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAA
* *
3886571 TTGGGAAATTGTTTGTTGACAACTACGTCCCTTCGTC
130 TTGAGAAATTGTTTGTTGACAACCACGTCCCTTCGTC
3886608 TGAAGTTGAA
1 TGAAGTTGAA
3886618 CTTGCGTTGT
Statistics
Matches: 167, Mismatches: 9, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
166 10 0.06
167 11 0.07
168 1 0.01
169 145 0.87
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.34
Consensus pattern (166 bp):
TGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTG
AAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAAT
TGAGAAATTGTTTGTTGACAACCACGTCCCTTCGTC
Found at i:3886543 original size:106 final size:105
Alignment explanation
Indices: 3886433--3887355 Score: 1209
Period size: 106 Copynumber: 8.9 Consensus size: 105
3886423 ACCAGCGGTC
*
3886433 CCTTCGTCATGAAGTTGAAATTGGCTCTGAAATTTGGAAGTTGTTTATTGACAACCAGCGGTCCC
1 CCTTCGTCGTGAAGTTGAAATTGGCTCTGAAA-TTGGAAGTTGTTTATTGACAACCAGCGGTCCC
*
3886498 TTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATAT
65 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* * *
3886539 CCTTCG-CTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACTA-C-GTCC
1 CCTTCGTC-GTGAAGTTGAAATTGGCTCTGAAATT-GGAAGTTGTTTATTGACAACCAGCGGTCC
3886601 CTTCGTC-TGAAGTTGAACTTGCGTTGTCTGGA-TCCAATAT
64 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* *
3886641 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATT-GAGAGTTGTTTGTTGACAACCAGCGGT-CC
1 CCTTCGTCGTGAAGTTGAAATTGGCTCTGAAATTGGA-AGTTGTTTATTGACAACCAGCGGTCCC
3886704 TTCGTCGTGAAGTTGAACTTGCGTTGTCT-G-GTCCAATAT
65 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* * * *
3886743 CCTTCGTTGTGAAGTTGAAATTGGCTTTGAAATTGAGAAGTTGTTTGTTGACAACCA---ATCCC
1 CCTTCGTCGTGAAGTTGAAATTGGCTCTGAAATTG-GAAGTTGTTTATTGACAACCAGCGGTCCC
* * *
3886805 TTCGTTGTGAAGTTGAACTTGCATTGTATGGAGTCCAATAT
65 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* *
3886846 CCTTC-AC-T---G-TG-AA-T---T-TGAAATTGGGAAGTTGTTTATTGACAACCAACGGTCCC
1 CCTTCGTCGTGAAGTTGAAATTGGCTCTGAAATT-GGAAGTTGTTTATTGACAACCAGCGGTCCC
*
3886899 TTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATAT
65 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* * * *
3886940 GCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTTTTTTTTGACAACCAGCGGTCCC
1 CCTTCGTCGTGAAGTTGAAATTGGCTCTGAAATTG-GAAGTTGTTTATTGACAACCAGCGGTCCC
*
3887005 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCTAATAT
65 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* *
3887046 CCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGGAATGTTGTTTATTGACAACCAGCGGTCCC
1 CCTTCGTCGTGAAGTTGAAATTGGCTCTGAAATTGGAA-GTTGTTTATTGACAACCAGCGGTCCC
* *
3887111 TTCGTCATGAAGTTGAACTTGTGTTGTCTGGAGTCCAATAT
65 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* * * *
3887152 CCTTC-ACTGTGAAGTTGAAATTGGATCTAAAATTGAGAAATTGTTTATTGACAACCAGCGGTCC
1 CCTTCGTC-GTGAAGTTGAAATTGGCTCTGAAATTG-GAAGTTGTTTATTGACAACCAGCGGTCC
3887216 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
64 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* * *
3887258 CCTTCG-CTGTGAAGTTGAAATTGGCTAC-GAAATTGGAAAATTG-TTGTTGACAACCAGCCGTC
1 CCTTCGTC-GTGAAGTTGAAATTGGCT-CTGAAATTGG-AAGTTGTTTATTGACAACCAGCGGTC
* * *
3887320 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGAGT
63 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
3887356 GGCAAGATAT
Statistics
Matches: 732, Mismatches: 49, Indels: 73
0.86 0.06 0.09
Matches are distributed among these distances:
91 27 0.04
92 2 0.00
94 45 0.06
95 1 0.00
96 3 0.00
97 2 0.00
98 1 0.00
99 1 0.00
100 5 0.01
101 48 0.07
102 93 0.13
103 81 0.11
104 13 0.02
105 60 0.08
106 346 0.47
107 4 0.01
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.35
Consensus pattern (105 bp):
CCTTCGTCGTGAAGTTGAAATTGGCTCTGAAATTGGAAGTTGTTTATTGACAACCAGCGGTCCCT
TCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
Found at i:3888041 original size:22 final size:22
Alignment explanation
Indices: 3888016--3888092 Score: 111
Period size: 22 Copynumber: 3.5 Consensus size: 22
3888006 TTATGTTTGG
*
3888016 TCAATGGTTTGGCATTTGATAC
1 TCAATGGTTTGGCATTTGATGC
* *
3888038 TCAAAGGTTTGGCATGTGATGC
1 TCAATGGTTTGGCATTTGATGC
3888060 TC-ATAGGTTTGGCATTTGATGC
1 TCAAT-GGTTTGGCATTTGATGC
3888082 TCAATGGTTTG
1 TCAATGGTTTG
3888093 ATGGGGTAGC
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
21 1 0.02
22 45 0.94
23 2 0.04
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.39
Consensus pattern (22 bp):
TCAATGGTTTGGCATTTGATGC
Found at i:3888723 original size:25 final size:25
Alignment explanation
Indices: 3888695--3888754 Score: 63
Period size: 24 Copynumber: 2.4 Consensus size: 25
3888685 TTTTTGTCCC
3888695 CTTTTCTTTTTGATT-TTTGTT-CTTT
1 CTTTTCTTTTT-ATTCTTTGTTGC-TT
* *
3888720 CTTTT-TTTTTCTTCTTTTTTGCTT
1 CTTTTCTTTTTATTCTTTGTTGCTT
3888744 CTTTTCTTTTT
1 CTTTTCTTTTT
3888755 TGTTTTTCCC
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
23 2 0.07
24 17 0.57
25 11 0.37
ACGTcount: A:0.02, C:0.15, G:0.05, T:0.78
Consensus pattern (25 bp):
CTTTTCTTTTTATTCTTTGTTGCTT
Found at i:3888752 original size:16 final size:15
Alignment explanation
Indices: 3888708--3888774 Score: 70
Period size: 14 Copynumber: 4.7 Consensus size: 15
3888698 TTCTTTTTGA
3888708 TTTTTGTTC-TTTCT
1 TTTTTGTTCTTTTCT
*
3888722 TTTTT-TT-TCTTCT
1 TTTTTGTTCTTTTCT
3888735 TTTTTGCTTCTTTTCT
1 TTTTTG-TTCTTTTCT
* *
3888751 TTTTTGTT-TTTCCC
1 TTTTTGTTCTTTTCT
3888765 TTTTTGTTCT
1 TTTTTGTTCT
3888775 GATTGAATCT
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
13 11 0.25
14 17 0.39
15 5 0.11
16 11 0.25
ACGTcount: A:0.00, C:0.16, G:0.06, T:0.78
Consensus pattern (15 bp):
TTTTTGTTCTTTTCT
Found at i:3888768 original size:29 final size:27
Alignment explanation
Indices: 3888709--3888774 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 27
3888699 TCTTTTTGAT
**
3888709 TTTTGTTCTTTCTTTTTTTTTCTTCTT
1 TTTTGTTCTTTCTTTTTTTTTCTTCCC
3888736 TTTTGCTTCTTTTCTTTTTTGTTT-TTCCC
1 TTTTG-TTC-TTTCTTTTTT-TTTCTTCCC
3888765 TTTTTGTTCT
1 -TTTTGTTCT
3888775 GATTGAATCT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
27 5 0.15
28 4 0.12
29 16 0.48
30 8 0.24
ACGTcount: A:0.00, C:0.17, G:0.06, T:0.77
Consensus pattern (27 bp):
TTTTGTTCTTTCTTTTTTTTTCTTCCC
Found at i:3890419 original size:15 final size:15
Alignment explanation
Indices: 3890399--3890427 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3890389 AGATCAGCCA
3890399 TTTGGATTCTCAGGC
1 TTTGGATTCTCAGGC
3890414 TTTGGATTCTCAGG
1 TTTGGATTCTCAGG
3890428 AGTTATCCTT
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:0.14, C:0.17, G:0.28, T:0.41
Consensus pattern (15 bp):
TTTGGATTCTCAGGC
Found at i:3893085 original size:27 final size:25
Alignment explanation
Indices: 3893047--3893101 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 25
3893037 ACAAAGTACG
*
3893047 AATAATATATATATATAAAATAAATA
1 AATAATAAATATATAT-AAATAAATA
*
3893073 AATAAGTAAATATATATAAATTAATA
1 AATAA-TAAATATATATAAATAAATA
3893099 AAT
1 AAT
3893102 TAAATGACGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 16 0.62
27 10 0.38
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.35
Consensus pattern (25 bp):
AATAATAAATATATATAAATAAATA
Found at i:3893100 original size:18 final size:17
Alignment explanation
Indices: 3893061--3893106 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
3893051 ATATATATAT
3893061 ATAAA-ATAAATAAATA
1 ATAAATATAAATAAATA
*
3893077 AGTAAATATATATAAATTA
1 A-TAAATATAAATAAA-TA
3893096 ATAAAT-TAAAT
1 ATAAATATAAAT
3893107 GACGAAAAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
16 1 0.04
17 8 0.32
18 13 0.52
19 3 0.12
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (17 bp):
ATAAATATAAATAAATA
Found at i:3893599 original size:9 final size:9
Alignment explanation
Indices: 3893552--3893725 Score: 58
Period size: 9 Copynumber: 18.8 Consensus size: 9
3893542 TATATAACAA
*
3893552 AATAAATAT
1 AATAAAAAT
*
3893561 TATAAAAAT
1 AATAAAAAT
3893570 AATACAAGTAAT
1 AATA-AA--AAT
3893582 AATACAAAAAT
1 AAT--AAAAAT
*
3893593 AATAAAAAG
1 AATAAAAAT
3893602 AA-AGAGAAAGT
1 AATA-A-AAA-T
3893613 -A-AAAAAT
1 AATAAAAAT
*
3893620 -ATAATAAT
1 AATAAAAAT
*
3893628 AATAATAAT
1 AATAAAAAT
3893637 AATAAAATAT
1 AATAAAA-AT
3893647 AA-AAAATAT
1 AATAAAA-AT
*
3893656 ACATATATAAT
1 A-ATA-AAAAT
* *
3893667 -ATAAATAG
1 AATAAAAAT
3893675 AATAAAAA-
1 AATAAAAAT
*
3893683 AA-AATAAT
1 AATAAAAAT
**
3893691 AGGAAAAAT
1 AATAAAAAT
3893700 AATAATAAAT
1 AATAA-AAAT
**
3893710 AATAGTAAT
1 AATAAAAAT
3893719 AATAAAA
1 AATAAAA
3893726 TGCAAAGAAA
Statistics
Matches: 126, Mismatches: 21, Indels: 36
0.69 0.11 0.20
Matches are distributed among these distances:
7 6 0.05
8 14 0.11
9 66 0.52
10 20 0.16
11 9 0.07
12 8 0.06
13 2 0.02
14 1 0.01
ACGTcount: A:0.69, C:0.02, G:0.05, T:0.24
Consensus pattern (9 bp):
AATAAAAAT
Found at i:3893628 original size:3 final size:3
Alignment explanation
Indices: 3893620--3893723 Score: 55
Period size: 3 Copynumber: 36.3 Consensus size: 3
3893610 AGTAAAAAAT
3893620 ATA ATA ATA ATA ATA ATA ATA A-A AT- ATA A-A A-A AT- ATA CATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA
* * ** *
3893661 TATA AT- ATA A-A TAGA ATA A-A A-A AAA ATA ATA GGA AAA ATA ATA
1 -ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
3893704 ATAA ATA ATA GTA ATA ATA A
1 AT-A ATA ATA ATA ATA ATA A
3893724 AATGCAAAGA
Statistics
Matches: 81, Mismatches: 10, Indels: 20
0.73 0.09 0.18
Matches are distributed among these distances:
2 17 0.21
3 54 0.67
4 10 0.12
ACGTcount: A:0.68, C:0.01, G:0.04, T:0.27
Consensus pattern (3 bp):
ATA
Found at i:3893679 original size:82 final size:83
Alignment explanation
Indices: 3893593--3893752 Score: 195
Period size: 82 Copynumber: 1.9 Consensus size: 83
3893583 ATACAAAAAT
*
3893593 AATAAAAAGAAAGAGAA-AGTAAAAAAT-ATAAT-AATAATAATAATAATAAAATATAAA-AAAT
1 AATAAAAA-AAA-AGAATAG-AAAAAATAATAATAAATAATAATAATAATAAAATACAAAGAAA-
*
3893654 ATACATATATA-ATATAAATAG
62 ATAAATATATATATATAAATAG
* * * *
3893675 AATAAAAAAAAATAATAGGAAAAATAATAATAAATAATAGTAATAATAAAATGCAAAGAAAATAA
1 AATAAAAAAAAAGAATAGAAAAAATAATAATAAATAATAATAATAATAAAATACAAAGAAAATAA
3893740 ATATATATATATA
66 ATATATATATATA
3893753 TAGGTAATAA
Statistics
Matches: 67, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
80 9 0.13
81 10 0.15
82 40 0.60
83 8 0.12
ACGTcount: A:0.68, C:0.01, G:0.06, T:0.24
Consensus pattern (83 bp):
AATAAAAAAAAAGAATAGAAAAAATAATAATAAATAATAATAATAATAAAATACAAAGAAAATAA
ATATATATATATAAATAG
Found at i:3893709 original size:22 final size:22
Alignment explanation
Indices: 3893675--3893725 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
3893665 ATATAAATAG
3893675 AATAAAAAAAAATAATAGGAAA
1 AATAAAAAAAAATAATAGGAAA
* * * *
3893697 AATAATAATAAATAATAGTAAT
1 AATAAAAAAAAATAATAGGAAA
3893719 AATAAAA
1 AATAAAA
3893726 TGCAAAGAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.22
Consensus pattern (22 bp):
AATAAAAAAAAATAATAGGAAA
Found at i:3894316 original size:37 final size:37
Alignment explanation
Indices: 3894275--3894380 Score: 158
Period size: 37 Copynumber: 2.9 Consensus size: 37
3894265 GTGCTTGTGG
* *
3894275 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTAAATCCTAGTAGAACTCT
* * *
3894312 ATCCTATTTTTAGGAGTTTAAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTAAATCCTAGTAGAACTCT
*
3894349 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGA
1 ATCCTATTTTTAGGAGTTTAAATCCTAGTAGA
3894381 CGAAAAGGTG
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 61 1.00
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTAAATCCTAGTAGAACTCT
Found at i:3896920 original size:30 final size:28
Alignment explanation
Indices: 3896886--3896960 Score: 84
Period size: 26 Copynumber: 2.7 Consensus size: 28
3896876 TTTTAATGAA
3896886 TATTTAATTTAGAATAATTAAATAATATTT
1 TATTTAATTT--AATAATTAAATAATATTT
*
3896916 TATTTCA--TAATAATTAAATAATATTT
1 TATTTAATTTAATAATTAAATAATATTT
* *
3896942 TAGTTAATTTGA-AATTAAA
1 TATTTAATTTAATAATTAAA
3896961 AACCCAAAAG
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
26 23 0.59
27 7 0.18
28 3 0.08
30 6 0.15
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.48
Consensus pattern (28 bp):
TATTTAATTTAATAATTAAATAATATTT
Found at i:3896927 original size:26 final size:25
Alignment explanation
Indices: 3896884--3896943 Score: 93
Period size: 26 Copynumber: 2.4 Consensus size: 25
3896874 TCTTTTAATG
*
3896884 AATATTTAATTTAGAATAATTAAAT
1 AATATTTTATTTAGAATAATTAAAT
*
3896909 AATATTTTATTTCATAATAATTAAAT
1 AATATTTTATTT-AGAATAATTAAAT
3896935 AATATTTTA
1 AATATTTTA
3896944 GTTAATTTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
25 11 0.34
26 21 0.66
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (25 bp):
AATATTTTATTTAGAATAATTAAAT
Found at i:3898300 original size:30 final size:30
Alignment explanation
Indices: 3898264--3898323 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
3898254 GAGAAGCTCA
3898264 CTCTTGGTTGAACCTTGGGTGTTTCCAGTG
1 CTCTTGGTTGAACCTTGGGTGTTTCCAGTG
3898294 CTCTTGGTTGAACCTTGGGTGTTTCCAGTG
1 CTCTTGGTTGAACCTTGGGTGTTTCCAGTG
3898324 ACTTAGGATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.10, C:0.20, G:0.30, T:0.40
Consensus pattern (30 bp):
CTCTTGGTTGAACCTTGGGTGTTTCCAGTG
Found at i:3906574 original size:28 final size:28
Alignment explanation
Indices: 3906542--3906604 Score: 126
Period size: 28 Copynumber: 2.2 Consensus size: 28
3906532 AAAAACATCG
3906542 AATGCATTTGATGCATCGATGCACCAGC
1 AATGCATTTGATGCATCGATGCACCAGC
3906570 AATGCATTTGATGCATCGATGCACCAGC
1 AATGCATTTGATGCATCGATGCACCAGC
3906598 AATGCAT
1 AATGCAT
3906605 CGATGCACTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (28 bp):
AATGCATTTGATGCATCGATGCACCAGC
Found at i:3906610 original size:94 final size:92
Alignment explanation
Indices: 3906476--3906657 Score: 242
Period size: 94 Copynumber: 2.0 Consensus size: 92
3906466 TTGAACATCG
* *
3906476 AATGCATTTCATGCATCGATGCACATACCATGCACCGATGCACTGAGGAT-TTTATGAAAAACAT
1 AATGCATTTCATGCATCGATGCACATACAATGCACCGATGCACTCAGGATATTT-TG--AAACAT
*
3906540 CGAATGCATTTGATGCATCGATGCACCAGC
63 CGAATGCACTTGATGCATCGATGCACCAGC
* * * * *
3906570 AATGCATTTGATGCATCGATGCACCA-GCAATGCATCGATGCACTCTGGGTATTTTGAAACATCG
1 AATGCATTTCATGCATCGATGCA-CATACAATGCACCGATGCACTCAGGATATTTTGAAACATCG
3906634 AATGCACTTGATGCATCGATGCAC
65 AATGCACTTGATGCATCGATGCAC
3906658 TCTTAGTGCA
Statistics
Matches: 78, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
92 31 0.40
94 42 0.54
95 5 0.06
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.26
Consensus pattern (92 bp):
AATGCATTTCATGCATCGATGCACATACAATGCACCGATGCACTCAGGATATTTTGAAACATCGA
ATGCACTTGATGCATCGATGCACCAGC
Found at i:3906657 original size:17 final size:19
Alignment explanation
Indices: 3906629--3906677 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
3906619 TATTTTGAAA
3906629 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
3906647 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
3906666 CACCGATGCACT
1 CATCGATGCACT
3906678 AAGGATCCGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:3912919 original size:21 final size:22
Alignment explanation
Indices: 3912895--3912938 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
3912885 CAATTCTTTT
3912895 TAAAAAAAATTA-ATTTCGAAA
1 TAAAAAAAATTAGATTTCGAAA
3912916 TAAAAAAAATTATGATTTCGAAA
1 TAAAAAAAATTA-GATTTCGAAA
3912939 ATTATTAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 12 0.57
23 9 0.43
ACGTcount: A:0.59, C:0.05, G:0.07, T:0.30
Consensus pattern (22 bp):
TAAAAAAAATTAGATTTCGAAA
Found at i:3914631 original size:2 final size:2
Alignment explanation
Indices: 3914624--3914652 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3914614 CAGCTTAAGC
3914624 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 T
3914653 CAATTGGCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3946064 original size:29 final size:29
Alignment explanation
Indices: 3946002--3946087 Score: 88
Period size: 29 Copynumber: 3.0 Consensus size: 29
3945992 AAAATCGAAA
* * *
3946002 ATTAAATGACTAAATAGG-AAAAATAGAT
1 ATTAAAGGACTAAATAGGTAAAAACAGAC
3946030 ATTTAAAGGACTAAA-AGGGTAAAAACAGAC
1 A-TTAAAGGACTAAATA-GGTAAAAACAGAC
*
3946060 ATTAAAAGGGCTAAATA-GTAAAAACAGA
1 ATT-AAAGGACTAAATAGGTAAAAACAGA
3946088 AACTAAAAAG
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
28 2 0.04
29 27 0.55
30 19 0.39
31 1 0.02
ACGTcount: A:0.56, C:0.07, G:0.17, T:0.20
Consensus pattern (29 bp):
ATTAAAGGACTAAATAGGTAAAAACAGAC
Found at i:3946068 original size:30 final size:28
Alignment explanation
Indices: 3946000--3946104 Score: 86
Period size: 29 Copynumber: 3.6 Consensus size: 28
3945990 CAAAAATCGA
* * *
3946000 AAATT-AAATGACTAAATAGGAAAAATAG
1 AAATTAAAAGGACTAAA-AGTAAAAACAG
* *
3946028 ATATTTAAAGGACTAAAAGGGTAAAAACAG
1 AAATTAAAAGGACTAAAA--GTAAAAACAG
* *
3946058 ACATTAAAAGGGCTAAATAGTAAAAACAG
1 AAATTAAAAGGACTAAA-AGTAAAAACAG
* *
3946087 AAACTAAAAAGACTAAAA
1 AAATTAAAAGGACTAAAA
3946105 CAATAATTAC
Statistics
Matches: 62, Mismatches: 11, Indels: 8
0.77 0.14 0.10
Matches are distributed among these distances:
28 6 0.10
29 33 0.53
30 22 0.35
31 1 0.02
ACGTcount: A:0.59, C:0.08, G:0.15, T:0.18
Consensus pattern (28 bp):
AAATTAAAAGGACTAAAAGTAAAAACAG
Found at i:3946252 original size:23 final size:23
Alignment explanation
Indices: 3946226--3946301 Score: 55
Period size: 23 Copynumber: 3.2 Consensus size: 23
3946216 CCTAAAGGAT
3946226 CAAACAATAATTAAATCAACTAC
1 CAAACAATAATTAAATCAACTAC
* * * ** *
3946249 CAAAGAGTGACTAAATAAA-AAAGGAT
1 CAAACA---A-TAATTAAATCAACTAC
3946275 CAAACAATAATTAAATCAACTAC
1 CAAACAATAATTAAATCAACTAC
3946298 CAAA
1 CAAA
3946302 GAGTGACTAA
Statistics
Matches: 36, Mismatches: 12, Indels: 10
0.62 0.21 0.17
Matches are distributed among these distances:
22 7 0.19
23 13 0.36
26 9 0.25
27 7 0.19
ACGTcount: A:0.58, C:0.17, G:0.07, T:0.18
Consensus pattern (23 bp):
CAAACAATAATTAAATCAACTAC
Found at i:3946291 original size:49 final size:50
Alignment explanation
Indices: 3946219--3946318 Score: 193
Period size: 49 Copynumber: 2.0 Consensus size: 50
3946209 ACCATAACCT
3946219 AAAGGATCAAACAATAATTAAATCAACTACCAAAGAGTGACT-AAATAAA
1 AAAGGATCAAACAATAATTAAATCAACTACCAAAGAGTGACTAAAATAAA
3946268 AAAGGATCAAACAATAATTAAATCAACTACCAAAGAGTGACTAAAATAAA
1 AAAGGATCAAACAATAATTAAATCAACTACCAAAGAGTGACTAAAATAAA
3946318 A
1 A
3946319 TATTTACAAC
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
49 42 0.84
50 8 0.16
ACGTcount: A:0.58, C:0.14, G:0.10, T:0.18
Consensus pattern (50 bp):
AAAGGATCAAACAATAATTAAATCAACTACCAAAGAGTGACTAAAATAAA
Found at i:3947659 original size:3 final size:3
Alignment explanation
Indices: 3947651--3947694 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
3947641 ATATGTATTG
* *
3947651 TAA TAA TAA TAA TAA TAA TAA TAG TAA TAA TAG TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
3947695 TAAATAAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:3948947 original size:15 final size:16
Alignment explanation
Indices: 3948923--3948966 Score: 56
Period size: 15 Copynumber: 2.8 Consensus size: 16
3948913 CTTACGATTA
*
3948923 TTATTATTCTTAT-TT
1 TTATTTTTCTTATATT
3948938 TTATTTTTCTTATATT
1 TTATTTTTCTTATATT
3948954 TT-TATTTTCTTAT
1 TTAT-TTTTCTTAT
3948967 GTGTAGGATG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 13 0.50
16 13 0.50
ACGTcount: A:0.18, C:0.07, G:0.00, T:0.75
Consensus pattern (16 bp):
TTATTTTTCTTATATT
Found at i:3948961 original size:16 final size:17
Alignment explanation
Indices: 3948933--3948966 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
3948923 TTATTATTCT
3948933 TATTTTTATTTTTCTTA
1 TATTTTTATTTTTCTTA
3948950 TATTTTTA-TTTTCTTA
1 TATTTTTATTTTTCTTA
3948966 T
1 T
3948967 GTGTAGGATG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (17 bp):
TATTTTTATTTTTCTTA
Done.