Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 3 of 198
Found at i:925871 original size:14 final size:15
Alignment explanation
Indices: 925849--925925 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
925839 CAATCAAACA
925849 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
925863 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
925878 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
925898 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
925912 ACGGAAAAT-ATTTT
1 CCAGAAAATCATTTT
925926 ACTGGCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 21 0.42
15 15 0.30
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:925890 original size:20 final size:20
Alignment explanation
Indices: 925865--925904 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
925855 AATATTTTCC
*
925865 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
925885 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
925905 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:925910 original size:34 final size:35
Alignment explanation
Indices: 925853--925919 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
925843 CAAACACCAG
*
925853 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
925888 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
925920 TATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:927923 original size:3 final size:3
Alignment explanation
Indices: 927915--927947 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
927905 AACCCCATAT
*
927915 CTC CTC CTC CTC TTC CTC CTC CTC CTC CTC CTC
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
927948 TTCTTCTTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.64, G:0.00, T:0.36
Consensus pattern (3 bp):
CTC
Found at i:929052 original size:3 final size:3
Alignment explanation
Indices: 929044--929074 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
929034 AAAACAGAAG
929044 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A
929075 AAAAGGAGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.32, G:0.00, T:0.32
Consensus pattern (3 bp):
ATC
Found at i:930980 original size:29 final size:28
Alignment explanation
Indices: 930926--930983 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
930916 TTATAGGGAC
*
930926 ATGGTCAAATTAATCCCTCTACTTTTAA
1 ATGGTCAAATTAATCCCTATACTTTTAA
* * *
930954 ATGGATCAATTTAATCCTTATATTTTTAA
1 ATGG-TCAAATTAATCCCTATACTTTTAA
930983 A
1 A
930984 AAAGAAACAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
28 4 0.16
29 21 0.84
ACGTcount: A:0.34, C:0.16, G:0.07, T:0.43
Consensus pattern (28 bp):
ATGGTCAAATTAATCCCTATACTTTTAA
Found at i:934277 original size:18 final size:17
Alignment explanation
Indices: 934233--934357 Score: 72
Period size: 17 Copynumber: 6.7 Consensus size: 17
934223 CGAATATAAT
*
934233 AAATATTTTTATTTTTA
1 AAATATTTTTAATTTTA
*
934250 AAATTTTTTTTAATTTTA
1 AAA-TATTTTTAATTTTA
* *
934268 AAATACTTTTAAAATACTTTTTTT
1 AAATA-TTTT----TA--ATTTTA
*
934292 AAATTTTTTTAATTTTA
1 AAATATTTTTAATTTTA
934309 AAATATTTTTAAAATACTTT-
1 AAATATTTTT--AAT--TTTA
* *
934329 TAATTTTTTTAATTTTA
1 AAATATTTTTAATTTTA
934346 AAATATTTTTAA
1 AAATATTTTTAA
934358 AATACTTTTT
Statistics
Matches: 82, Mismatches: 13, Indels: 26
0.68 0.11 0.21
Matches are distributed among these distances:
16 3 0.04
17 27 0.33
18 22 0.27
19 5 0.06
20 8 0.10
21 3 0.04
22 2 0.02
23 4 0.05
24 8 0.10
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (17 bp):
AAATATTTTTAATTTTA
Found at i:934277 original size:19 final size:18
Alignment explanation
Indices: 934238--934277 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
934228 ATAATAAATA
* *
934238 TTTTTATTTTTAAAATTT
1 TTTTTAATTTTAAAATCT
934256 TTTTTAATTTTAAAATACT
1 TTTTTAATTTTAAAAT-CT
934275 TTT
1 TTT
934278 AAAATACTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTTTAATTTTAAAATCT
Found at i:934329 original size:28 final size:29
Alignment explanation
Indices: 934274--934335 Score: 81
Period size: 28 Copynumber: 2.1 Consensus size: 29
934264 TTTAAAATAC
* **
934274 TTTTAAAATACTTTTTTTAAATTTTTTTAA
1 TTTTAAAATAC-TTTTTAAAATACTTTTAA
934304 TTTTAAAATA-TTTTTAAAATACTTTTAA
1 TTTTAAAATACTTTTTAAAATACTTTTAA
934332 TTTT
1 TTTT
934336 TTTAATTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 19 0.66
30 10 0.34
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.61
Consensus pattern (29 bp):
TTTTAAAATACTTTTTAAAATACTTTTAA
Found at i:934369 original size:13 final size:11
Alignment explanation
Indices: 934263--934377 Score: 58
Period size: 11 Copynumber: 11.3 Consensus size: 11
934253 TTTTTTTTAA
*
934263 TTTTAAAATAC
1 TTTTAAAATAT
934274 TTTTAAAATACTT
1 TTTTAAAATA--T
*
934287 TTTTTAAAT-T
1 TTTTAAAATAT
*
934297 TTTT----TAA
1 TTTTAAAATAT
934304 TTTTAAAATAT
1 TTTTAAAATAT
*
934315 TTTTAAAATAC
1 TTTTAAAATAT
934326 TTTT--AAT-T
1 TTTTAAAATAT
*
934334 TTTT----TAA
1 TTTTAAAATAT
934341 TTTTAAAATAT
1 TTTTAAAATAT
934352 TTTTAAAATACTT
1 TTTTAAAATA--T
934365 TTTTAAAAT-T
1 TTTTAAAATAT
934375 TTT
1 TTT
934378 GTTTTAATTT
Statistics
Matches: 82, Mismatches: 8, Indels: 29
0.69 0.07 0.24
Matches are distributed among these distances:
6 2 0.02
7 8 0.10
8 4 0.05
9 3 0.04
10 9 0.11
11 38 0.46
13 18 0.22
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.59
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:934419 original size:26 final size:26
Alignment explanation
Indices: 934368--934419 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
934358 AATACTTTTT
**
934368 TAAAATTTTTGTTTTAATTTTTAAAA
1 TAAAATTTTTGTTTTAATTTAAAAAA
*
934394 TAAATTTTTTGTATTT-ATTTAAAAAA
1 TAAAATTTTTGT-TTTAATTTAAAAAA
934420 CGGGCCGGGC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 19 0.86
27 3 0.14
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (26 bp):
TAAAATTTTTGTTTTAATTTAAAAAA
Found at i:934833 original size:14 final size:14
Alignment explanation
Indices: 934816--934844 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
934806 GCTCGTGTGG
934816 CCCACACCACCATA
1 CCCACACCACCATA
934830 CCCACACCACCATA
1 CCCACACCACCATA
934844 C
1 C
934845 TGCCGTGTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.59, G:0.00, T:0.07
Consensus pattern (14 bp):
CCCACACCACCATA
Found at i:935174 original size:40 final size:40
Alignment explanation
Indices: 935128--935206 Score: 158
Period size: 40 Copynumber: 2.0 Consensus size: 40
935118 TACTAAACCG
935128 TACTCCACAATCAAACCAAAAGGAGAACTCGACAATTCCC
1 TACTCCACAATCAAACCAAAAGGAGAACTCGACAATTCCC
935168 TACTCCACAATCAAACCAAAAGGAGAACTCGACAATTCC
1 TACTCCACAATCAAACCAAAAGGAGAACTCGACAATTCC
935207 AACAGCACGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.43, C:0.32, G:0.10, T:0.15
Consensus pattern (40 bp):
TACTCCACAATCAAACCAAAAGGAGAACTCGACAATTCCC
Found at i:937173 original size:2 final size:2
Alignment explanation
Indices: 937166--937211 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
937156 GATTGAAATA
*
937166 AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
937208 AT AT
1 AT AT
937212 TTGCTTACAC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:937380 original size:24 final size:24
Alignment explanation
Indices: 937348--937395 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
937338 GTTGTGTCTA
937348 AGACTTTGGGACATATCATGAGGC
1 AGACTTTGGGACATATCATGAGGC
*
937372 AGACTTTGGGATATATCATGAGGC
1 AGACTTTGGGACATATCATGAGGC
937396 TGACGCCATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.29, C:0.15, G:0.29, T:0.27
Consensus pattern (24 bp):
AGACTTTGGGACATATCATGAGGC
Found at i:937684 original size:31 final size:30
Alignment explanation
Indices: 937635--937710 Score: 98
Period size: 31 Copynumber: 2.5 Consensus size: 30
937625 CCAAAAAAAA
*
937635 TTTAGGAAAATTCTATTTCCCGCTTGAAATT
1 TTTA-GAAAATTTTATTTCCCGCTTGAAATT
* * *
937666 TTTAGAAAATTTTCATTTCTCTCTTGAAGTT
1 TTTAGAAAATTTT-ATTTCCCGCTTGAAATT
937697 TTTAGAAAATTTTA
1 TTTAGAAAATTTTA
937711 ATTAGTCCCC
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
30 9 0.22
31 31 0.77
ACGTcount: A:0.30, C:0.12, G:0.11, T:0.47
Consensus pattern (30 bp):
TTTAGAAAATTTTATTTCCCGCTTGAAATT
Found at i:946762 original size:3 final size:3
Alignment explanation
Indices: 946754--946816 Score: 119
Period size: 3 Copynumber: 21.3 Consensus size: 3
946744 ATTTCTTTCC
946754 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
946802 TTA TTA TTA TT- TTA T
1 TTA TTA TTA TTA TTA T
946817 GAATCGGATC
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 57 0.97
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:947316 original size:13 final size:13
Alignment explanation
Indices: 947295--947328 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
947285 TTAGGGTTCA
947295 AGTTTGGGTTT-G
1 AGTTTGGGTTTGG
947307 AGTTTCGGGTTTGG
1 AGTTT-GGGTTTGG
947321 AGTTTGGG
1 AGTTTGGG
947329 GTTCAAGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 5 0.25
13 9 0.45
14 6 0.30
ACGTcount: A:0.09, C:0.03, G:0.44, T:0.44
Consensus pattern (13 bp):
AGTTTGGGTTTGG
Found at i:947409 original size:30 final size:30
Alignment explanation
Indices: 947375--947440 Score: 132
Period size: 30 Copynumber: 2.2 Consensus size: 30
947365 AATGAGATGA
947375 AAAAAATTGTTGAAATATAATTAAATAATT
1 AAAAAATTGTTGAAATATAATTAAATAATT
947405 AAAAAATTGTTGAAATATAATTAAATAATT
1 AAAAAATTGTTGAAATATAATTAAATAATT
947435 AAAAAA
1 AAAAAA
947441 GAACCATGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (30 bp):
AAAAAATTGTTGAAATATAATTAAATAATT
Found at i:947481 original size:55 final size:54
Alignment explanation
Indices: 947421--947536 Score: 137
Period size: 55 Copynumber: 2.1 Consensus size: 54
947411 TTGTTGAAAT
947421 ATAATTAAAT-AATT-AAAAAAGAACCATGAATGATGTGGTGGGAAGGGTCCATAAA
1 ATAATT-AATCAATTAAAAAAAG-A-CATGAATGATGTGGTGGGAAGGGTCCATAAA
** ** *
947476 ATAATTTCTCCGTTAAAAAAATGATATGAATGATGTGGTGGGAAGGGTCCATAAA
1 ATAATTAATCAATTAAAAAAA-GACATGAATGATGTGGTGGGAAGGGTCCATAAA
947531 ATAATT
1 ATAATT
947537 TCTCCGTTAA
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
54 1 0.02
55 44 0.83
56 7 0.13
57 1 0.02
ACGTcount: A:0.43, C:0.08, G:0.22, T:0.28
Consensus pattern (54 bp):
ATAATTAATCAATTAAAAAAAGACATGAATGATGTGGTGGGAAGGGTCCATAAA
Found at i:947537 original size:55 final size:55
Alignment explanation
Indices: 947446--947551 Score: 212
Period size: 55 Copynumber: 1.9 Consensus size: 55
947436 AAAAAGAACC
947446 ATGAATGATGTGGTGGGAAGGGTCCATAAAATAATTTCTCCGTTAAAAAAATGAT
1 ATGAATGATGTGGTGGGAAGGGTCCATAAAATAATTTCTCCGTTAAAAAAATGAT
947501 ATGAATGATGTGGTGGGAAGGGTCCATAAAATAATTTCTCCGTTAAAAAAA
1 ATGAATGATGTGGTGGGAAGGGTCCATAAAATAATTTCTCCGTTAAAAAAA
947552 AAAAGATTAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 51 1.00
ACGTcount: A:0.39, C:0.09, G:0.24, T:0.28
Consensus pattern (55 bp):
ATGAATGATGTGGTGGGAAGGGTCCATAAAATAATTTCTCCGTTAAAAAAATGAT
Found at i:951143 original size:115 final size:116
Alignment explanation
Indices: 950941--951177 Score: 395
Period size: 115 Copynumber: 2.1 Consensus size: 116
950931 ACGTGCTGCC
* *
950941 TGCATAACAGCATAACGGTCATTGTACTAGCTTCCTTCTCCACATATTCTGAATTCTTGCTATAT
1 TGCATAACAGCATAACGGCCATTGTACTAGCTTCCTTCTCCACATATTCCGAATTCTTGCTATAT
*
951006 TATTAGTATGAACTCACCAT-AAAAAACACCTTGATCTTAGCAGGCACCAA
66 TATCAGTATGAACTCACCATAAAAAAACACCTTGATCTTAGCAGGCACCAA
* * *
951056 TGCATAACGGCATAATGGCCGTTGTACTAGCTTCCTTCTCCACATATTCCGAATTCTTGCTATAT
1 TGCATAACAGCATAACGGCCATTGTACTAGCTTCCTTCTCCACATATTCCGAATTCTTGCTATAT
*
951121 TATCAGTATGAACTCTCCATAAAAAAACACCTTGATCTTAGCAGGCACCAA
66 TATCAGTATGAACTCACCATAAAAAAACACCTTGATCTTAGCAGGCACCAA
*
951172 TACATA
1 TGCATA
951178 TCCACTTCCA
Statistics
Matches: 113, Mismatches: 8, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
115 78 0.69
116 35 0.31
ACGTcount: A:0.32, C:0.25, G:0.13, T:0.31
Consensus pattern (116 bp):
TGCATAACAGCATAACGGCCATTGTACTAGCTTCCTTCTCCACATATTCCGAATTCTTGCTATAT
TATCAGTATGAACTCACCATAAAAAAACACCTTGATCTTAGCAGGCACCAA
Found at i:954209 original size:26 final size:25
Alignment explanation
Indices: 954177--954225 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
954167 TCGAAAATAT
**
954177 ATGAAAATTTTATATAAAATATAAAA
1 ATGAAAATAATATA-AAAATATAAAA
954203 ATGAAAATAATATAAAAATATAA
1 ATGAAAATAATATAAAAATATAA
954226 TAAAATTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 9 0.43
26 12 0.57
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (25 bp):
ATGAAAATAATATAAAAATATAAAA
Found at i:962248 original size:101 final size:102
Alignment explanation
Indices: 962036--962250 Score: 398
Period size: 101 Copynumber: 2.1 Consensus size: 102
962026 ATAGGAAGAG
* *
962036 GGAGAAG-GAAAGAGATTGGAGCAGGGGTAATGACAGAGAAAGAGTTGGGAAAAAATGTAAAAAA
1 GGAGAAGTGACAGAGATTGGAGCAGGGGTAATGACAGAGAAAGAGTTGGGAAAAAAGGTAAAAAA
962100 AAAACTGAAGAATGGAACCGAAAGCAGGAGAGGGAAA
66 AAAACTGAAGAATGGAACCGAAAGCAGGAGAGGGAAA
962137 GGAGAAGTGACAGAGATTGGAGCAGGGGTAATGACAGAGAAAGAGTTGGGAAAAAAGGT-AAAAA
1 GGAGAAGTGACAGAGATTGGAGCAGGGGTAATGACAGAGAAAGAGTTGGGAAAAAAGGTAAAAAA
962201 AAAACTGAAGAATGGAACCGAAAGCAGGAGAGGGAAA
66 AAAACTGAAGAATGGAACCGAAAGCAGGAGAGGGAAA
962238 GGAGAAGTGACAG
1 GGAGAAGTGACAG
962251 GAGTAGGGAT
Statistics
Matches: 111, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
101 62 0.56
102 49 0.44
ACGTcount: A:0.48, C:0.07, G:0.36, T:0.10
Consensus pattern (102 bp):
GGAGAAGTGACAGAGATTGGAGCAGGGGTAATGACAGAGAAAGAGTTGGGAAAAAAGGTAAAAAA
AAAACTGAAGAATGGAACCGAAAGCAGGAGAGGGAAA
Found at i:971429 original size:2 final size:2
Alignment explanation
Indices: 971422--971459 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
971412 AGTACTAACC
971422 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
971460 GAAGTTTTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:971667 original size:23 final size:25
Alignment explanation
Indices: 971641--971688 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
971631 CATTTTATGT
971641 TTATATAT-TGC-ATATAAAAATAA
1 TTATATATCTGCAATATAAAAATAA
* *
971664 TTATATTTCTTCAATATAAAAATAA
1 TTATATATCTGCAATATAAAAATAA
971689 ATTGATGTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 7 0.33
24 2 0.10
25 12 0.57
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (25 bp):
TTATATATCTGCAATATAAAAATAA
Found at i:974185 original size:126 final size:125
Alignment explanation
Indices: 973847--974201 Score: 454
Period size: 119 Copynumber: 2.9 Consensus size: 125
973837 CTAACCTGAG
* * **
973847 AAGAATCATCACTAGTAAACATTGAAAGTGCAACTGCTATGCTAGTGCAATGAAGAACATATTGA
1 AAGAATCATCACTAGTAAACA-TCAAAGTGCAACCGCTATGCTAGTGCAATGAAGAACATATCAA
* * *
973912 CATTGAACTCGAGATACGCAAAAGAATGACAACATATGCAGCAAATAGCATAAGAACCGGA
65 CATTAAACTCGAGATATGCAAAAGAATAACAACATATGCAGCAAATAGCATAAGAACCGGA
* * * *
973973 AAGAACCATCACTAGTAAACATC--A----AACCACTATGCTAGTGCAATAAAGAACATATCACC
1 AAGAATCATCACTAGTAAACATCAAAGTGCAACCGCTATGCTAGTGCAATGAAGAACATATCAAC
* ** *
974032 ATTAAACTCGAGATATGCAAACA-AATAACAACATATGCAGCAAATTGTGTAAGAACTGGA
66 ATTAAACTCGAGATATGCAAA-AGAATAACAACATATGCAGCAAATAGCATAAGAACCGGA
*
974092 AAGAATCATCACTAGTATACATCAAAAGTGCAACCGCTATGCTAGTGCAATGAAGAACATATCAA
1 AAGAATCATCACTAGTAAACATC-AAAGTGCAACCGCTATGCTAGTGCAATGAAGAACATATCAA
* * * *
974157 CATTAAACTTGAGATATGCAAATGAATAATAACATATGCATCAAA
65 CATTAAACTCGAGATATGCAAAAGAATAACAACATATGCAGCAAA
974202 ATCGTATGAG
Statistics
Matches: 196, Mismatches: 24, Indels: 18
0.82 0.10 0.08
Matches are distributed among these distances:
119 101 0.52
120 1 0.01
122 1 0.01
123 1 0.01
125 1 0.01
126 91 0.46
ACGTcount: A:0.45, C:0.18, G:0.15, T:0.21
Consensus pattern (125 bp):
AAGAATCATCACTAGTAAACATCAAAGTGCAACCGCTATGCTAGTGCAATGAAGAACATATCAAC
ATTAAACTCGAGATATGCAAAAGAATAACAACATATGCAGCAAATAGCATAAGAACCGGA
Found at i:980321 original size:31 final size:31
Alignment explanation
Indices: 980255--980326 Score: 74
Period size: 31 Copynumber: 2.3 Consensus size: 31
980245 GTCTTTAGAA
* *
980255 TATTTAAAAGTTTTTAATTAAGTCATTAAAG
1 TATTTAAAAGTTTTTAATTAAGTCACTAAAC
* * *
980286 TATTT-AAAGTTTTTCATTTAAGTTACTGAAC
1 TATTTAAAAGTTTTT-AATTAAGTCACTAAAC
980317 TATTTGAAAA
1 TATTT-AAAA
980327 TGAGTTAAGT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
30 9 0.27
31 21 0.64
33 3 0.09
ACGTcount: A:0.39, C:0.06, G:0.10, T:0.46
Consensus pattern (31 bp):
TATTTAAAAGTTTTTAATTAAGTCACTAAAC
Found at i:982919 original size:18 final size:17
Alignment explanation
Indices: 982896--982930 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
982886 GAATAGATTT
982896 TTAATTAAATAAATTTAA
1 TTAATTAAA-AAATTTAA
982914 TTAATTAAAAAATTTAA
1 TTAATTAAAAAATTTAA
982931 ACCCTAAACC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TTAATTAAAAAATTTAA
Found at i:983768 original size:18 final size:17
Alignment explanation
Indices: 983737--983771 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
983727 GATTTAGGGT
983737 TTAAATTTTTTAATTAA
1 TTAAATTTTTTAATTAA
983754 TTAAATTTATTTAATTAA
1 TTAAATTT-TTTAATTAA
983772 AAATCACTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTAAATTTTTTAATTAA
Found at i:989806 original size:2 final size:2
Alignment explanation
Indices: 989799--989829 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
989789 TTGTGTTGCT
*
989799 TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
989830 CATGGACTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:991438 original size:17 final size:17
Alignment explanation
Indices: 991410--991455 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
991400 ATTATAAAAT
991410 AAAAT-AAAATAAA-TA
1 AAAATCAAAATAAATTA
*
991425 TAAATCACAAATAAATTA
1 AAAATCA-AAATAAATTA
991443 AAAATCAAAATAA
1 AAAATCAAAATAA
991456 TCCAAACTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 4 0.15
16 1 0.04
17 13 0.50
18 8 0.31
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.22
Consensus pattern (17 bp):
AAAATCAAAATAAATTA
Found at i:991457 original size:27 final size:26
Alignment explanation
Indices: 991406--991461 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 26
991396 AACAATTATA
991406 AAATAAAATAAAATAAATATAAATCAC
1 AAATAAAATAAAATAAATATAAATC-C
*
991433 AAATAAATTAAAAATCAAA-AT-AATCC
1 AAATAAAAT-AAAAT-AAATATAAATCC
991459 AAA
1 AAA
991462 CTAGAAACAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
26 4 0.15
27 12 0.46
28 7 0.27
29 3 0.12
ACGTcount: A:0.70, C:0.09, G:0.00, T:0.21
Consensus pattern (26 bp):
AAATAAAATAAAATAAATATAAATCC
Found at i:992317 original size:4 final size:4
Alignment explanation
Indices: 992303--992335 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
992293 GAATTTCATG
*
992303 ACAT GCAT ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
992336 TGTATCACTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.48, C:0.24, G:0.03, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:1007743 original size:31 final size:28
Alignment explanation
Indices: 1007704--1007789 Score: 82
Period size: 31 Copynumber: 2.9 Consensus size: 28
1007694 AAGAAGTTTG
1007704 AGGATTAAATTGATAGAATTTGTAAATAT
1 AGGATTAAATTGATAGAATTTGTAAAT-T
* * * *
1007733 GAAGGGTTAAATTTATTGAATTATTTAGAATT
1 --AGGATTAAATTGATAGAATT-TGTA-AATT
*
1007765 AGGATTAAATTGATAGAATATGTAA
1 AGGATTAAATTGATAGAATTTGTAA
1007790 GTATTGAGGA
Statistics
Matches: 44, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
28 1 0.02
29 3 0.07
30 16 0.36
31 17 0.39
32 4 0.09
33 3 0.07
ACGTcount: A:0.43, C:0.00, G:0.19, T:0.38
Consensus pattern (28 bp):
AGGATTAAATTGATAGAATTTGTAAATT
Found at i:1012418 original size:95 final size:92
Alignment explanation
Indices: 1012299--1012675 Score: 464
Period size: 95 Copynumber: 4.1 Consensus size: 92
1012289 TAATTTAAAA
* * *
1012299 AAACCATACATATACATATACATATACATGTGCAAATAGTAATCATCATATAAAAAAAAATCAAA
1 AAACTATACATACACATATACATATACAT-T-C-AATAGTAATCATCATATAAAAAAACATCAAA
1012364 CTAGCATATAGTATTGATCATAGATTCAAT
63 CTAGCATATAGTATTGATCATAGATTCAAT
* * *
1012394 GAACTAAACATACACATATTCATATACATATACATATAGTAATCATCATATAAAAAAACATCAAA
1 AAACTATACATACACATATACATATACAT-T-CA-ATAGTAATCATCATATAAAAAAACATCAAA
1012459 CTAGCATATAGTATTGATCATAGATTCAAT
63 CTAGCATATAGTATTGATCATAGATTCAAT
*
1012489 AAACTATACATACACAT-TCACATATACA-T--ATAGTAATCATCATATAAAAGAACATCAAACT
1 AAACTATACATACACATAT-ACATATACATTCAATAGTAATCATCATATAAAAAAACATCAAACT
1012550 AGCATATAGTATTGATCATAGATTCAAT
65 AGCATATAGTATTGATCATAGATTCAAT
* * * * *
1012578 AAACTATACATACACATACATATATACATAT-ATAGTAGTTATTAT-ATAGAAAAACAACATCAA
1 AAACTATACATACACATATACATATACAT-TCA-A-TAGTAATCATCATATAAAAA-AACATCAA
* * *
1012641 ACTA--ATATAGCACTGATCAAAGATTCAAT
62 ACTAGCATATAGTATTGATCATAGATTCAAT
1012670 AAACTA
1 AAACTA
1012676 AATAGATGTG
Statistics
Matches: 252, Mismatches: 21, Indels: 21
0.86 0.07 0.07
Matches are distributed among these distances:
89 84 0.33
91 1 0.00
92 28 0.11
93 9 0.04
94 22 0.09
95 108 0.43
ACGTcount: A:0.49, C:0.16, G:0.07, T:0.29
Consensus pattern (92 bp):
AAACTATACATACACATATACATATACATTCAATAGTAATCATCATATAAAAAAACATCAAACTA
GCATATAGTATTGATCATAGATTCAAT
Found at i:1012558 original size:89 final size:89
Alignment explanation
Indices: 1012334--1012675 Score: 463
Period size: 89 Copynumber: 3.7 Consensus size: 89
1012324 ACATGTGCAA
* *
1012334 ATAGTAATCATCATATAAAAAAAAATCAAACTAGCATATAGTATTGATCATAGATTCAATGAACT
1 ATAGTAATCATCATATAAAAAAACATCAAACTAGCATATAGTATTGATCATAGATTCAATAAACT
*
1012399 AAACATACACATATTCATATACATATACAT
66 ATACATACAC--ATTC----ACATATACAT
1012429 ATAGTAATCATCATATAAAAAAACATCAAACTAGCATATAGTATTGATCATAGATTCAATAAACT
1 ATAGTAATCATCATATAAAAAAACATCAAACTAGCATATAGTATTGATCATAGATTCAATAAACT
1012494 ATACATACACATTCACATATACAT
66 ATACATACACATTCACATATACAT
*
1012518 ATAGTAATCATCATATAAAAGAACATCAAACTAGCATATAGTATTGATCATAGATTCAATAAACT
1 ATAGTAATCATCATATAAAAAAACATCAAACTAGCATATAGTATTGATCATAGATTCAATAAACT
* *
1012583 ATACATACACATACATATATACATAT
66 ATACATACACATTCACATATAC--AT
* * * * * *
1012609 ATAGTAGTTATTATATAGAAAAACAACATCAAACTA--ATATAGCACTGATCAAAGATTCAATAA
1 ATAGTAATCATCATAT--AAAAA-AACATCAAACTAGCATATAGTATTGATCATAGATTCAATAA
1012672 ACTA
63 ACTA
1012676 AATAGATGTG
Statistics
Matches: 229, Mismatches: 13, Indels: 13
0.90 0.05 0.05
Matches are distributed among these distances:
89 94 0.41
91 15 0.07
92 28 0.12
93 8 0.03
94 12 0.05
95 72 0.31
ACGTcount: A:0.49, C:0.15, G:0.07, T:0.29
Consensus pattern (89 bp):
ATAGTAATCATCATATAAAAAAACATCAAACTAGCATATAGTATTGATCATAGATTCAATAAACT
ATACATACACATTCACATATACAT
Found at i:1013769 original size:3 final size:3
Alignment explanation
Indices: 1013763--1013793 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
1013753 TCACCACCGT
*
1013763 CTC CTC CTC CTC CTC CTC CTC CTC CAC CTC C
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC C
1013794 GCCGCCGGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.03, C:0.68, G:0.00, T:0.29
Consensus pattern (3 bp):
CTC
Found at i:1015430 original size:66 final size:65
Alignment explanation
Indices: 1015375--1015503 Score: 181
Period size: 66 Copynumber: 2.0 Consensus size: 65
1015365 CATGTTTTAT
1015375 ACAATGCCTATAACTATACATAATG-T-CTCCCCAACCCTTAAATAAGAGAATAATGGGCTTCAG
1 ACAATGCCTATAACTATACAT-A-GCTCCTCCCCAACCCTTAAATAAGAGAATAATGGGCTTCAG
1015438 TGC
64 T-C
* * * *
1015441 ACGATGCTTATAACTATACATAGCTCCTCCCCAACCCTTAAATAAGAGGATAATGCGCTTCAG
1 ACAATGCCTATAACTATACATAGCTCCTCCCCAACCCTTAAATAAGAGAATAATGGGCTTCAG
1015504 CGCACTCGAA
Statistics
Matches: 57, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
64 1 0.02
65 2 0.04
66 54 0.95
ACGTcount: A:0.35, C:0.26, G:0.14, T:0.26
Consensus pattern (65 bp):
ACAATGCCTATAACTATACATAGCTCCTCCCCAACCCTTAAATAAGAGAATAATGGGCTTCAGTC
Found at i:1015951 original size:21 final size:19
Alignment explanation
Indices: 1015910--1015951 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
1015900 TTTATTAATT
*
1015910 TATATATTTTAATTTTAAA
1 TATATATTTTAATTTCAAA
1015929 TATATATATTTAATTTCATAA
1 TATATAT-TTTAATTTCA-AA
1015950 TA
1 TA
1015952 ATAATATAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 7 0.35
20 9 0.45
21 4 0.20
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (19 bp):
TATATATTTTAATTTCAAA
Found at i:1019652 original size:29 final size:30
Alignment explanation
Indices: 1019592--1019664 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 30
1019582 CAAAAACTAC
* * *
1019592 ACATGAACTATGGTTTAATGTGCAGTTGTAT
1 ACATGAATTTTGGTTT-ATGTGCAATTGTAT
*
1019623 ACATGAATTTTGGTTT-TGTGCAATTTTAT
1 ACATGAATTTTGGTTTATGTGCAATTGTAT
1019652 ACATGAAATTTTG
1 ACATG-AATTTTG
1019665 ATTTGATCCA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
29 16 0.43
30 7 0.19
31 14 0.38
ACGTcount: A:0.29, C:0.08, G:0.19, T:0.44
Consensus pattern (30 bp):
ACATGAATTTTGGTTTATGTGCAATTGTAT
Found at i:1019677 original size:30 final size:29
Alignment explanation
Indices: 1019620--1019677 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
1019610 TGTGCAGTTG
* *
1019620 TATACATGAATTTTGGTTTTGTGCAATTT
1 TATACATGAATTTTGGATTTGTCCAATTT
1019649 TATACATGAAATTTT-GATTTGATCCAATT
1 TATACATG-AATTTTGGATTTG-TCCAATT
1019678 CTTGTAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 13 0.52
30 12 0.48
ACGTcount: A:0.29, C:0.09, G:0.14, T:0.48
Consensus pattern (29 bp):
TATACATGAATTTTGGATTTGTCCAATTT
Found at i:1020849 original size:18 final size:20
Alignment explanation
Indices: 1020817--1020856 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
1020807 TCCTAATTCT
*
1020817 AAAAATTAAAGAAATATATA
1 AAAAATTAAAGAAATACATA
1020837 AAAAATT-AA-AAATACATA
1 AAAAATTAAAGAAATACATA
1020855 AA
1 AA
1020857 TATTTTCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 10 0.53
19 2 0.11
20 7 0.37
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.23
Consensus pattern (20 bp):
AAAAATTAAAGAAATACATA
Found at i:1024748 original size:21 final size:21
Alignment explanation
Indices: 1024724--1024769 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1024714 AAATAAATAG
1024724 ATAATTCATGAAGTTAAA-AAA
1 ATAATTC-TGAAGTTAAAGAAA
* *
1024745 ATAATTCTTAATTTAAAGAAA
1 ATAATTCTGAAGTTAAAGAAA
1024766 ATAA
1 ATAA
1024770 ATGTAATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.57, C:0.04, G:0.07, T:0.33
Consensus pattern (21 bp):
ATAATTCTGAAGTTAAAGAAA
Found at i:1028175 original size:2 final size:2
Alignment explanation
Indices: 1028168--1028203 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1028158 TAAAAACCTG
1028168 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1028204 GGCACTTAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1028422 original size:23 final size:22
Alignment explanation
Indices: 1028388--1028431 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
1028378 ATGCTTTATG
1028388 TTTTTTATTATTCAAGATTAGT
1 TTTTTTATTATTCAAGATTAGT
* *
1028410 TTTTCTTATTATTTATGATTAG
1 TTTT-TTATTATTCAAGATTAG
1028432 AATTTTAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.25, C:0.05, G:0.09, T:0.61
Consensus pattern (22 bp):
TTTTTTATTATTCAAGATTAGT
Found at i:1037994 original size:29 final size:32
Alignment explanation
Indices: 1037956--1038019 Score: 80
Period size: 30 Copynumber: 2.1 Consensus size: 32
1037946 CTACATAAAA
*
1037956 TTTGATTAAAATATGTAAT-TAGTCCCT-TAT
1 TTTGATTAAAATATGCAATATAGTCCCTATAT
* *
1037986 TTTGA-TAAAGTTTGCAATATAGTCCCTATAT
1 TTTGATTAAAATATGCAATATAGTCCCTATAT
1038017 TTT
1 TTT
1038020 AAAAGTAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
29 10 0.34
30 13 0.45
31 6 0.21
ACGTcount: A:0.31, C:0.11, G:0.11, T:0.47
Consensus pattern (32 bp):
TTTGATTAAAATATGCAATATAGTCCCTATAT
Found at i:1040038 original size:21 final size:21
Alignment explanation
Indices: 1040014--1040056 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1040004 AATATAAAAC
*
1040014 TATCTTAAAGATAAATAATAT
1 TATCATAAAGATAAATAATAT
* *
1040035 TATCATAAATATAAATATTAT
1 TATCATAAAGATAAATAATAT
1040056 T
1 T
1040057 TAATTATCAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (21 bp):
TATCATAAAGATAAATAATAT
Found at i:1040062 original size:26 final size:26
Alignment explanation
Indices: 1040033--1040084 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
1040023 GATAAATAAT
*
1040033 ATTATCATAAATATAAATATTATTTA
1 ATTATCATAAAGATAAATATTATTTA
*
1040059 ATTATCATTAAGATAAATATTATTTA
1 ATTATCATAAAGATAAATATTATTTA
1040085 TCTTAATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (26 bp):
ATTATCATAAAGATAAATATTATTTA
Found at i:1040660 original size:15 final size:16
Alignment explanation
Indices: 1040635--1040665 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
1040625 AATTGACATG
1040635 AGAATTTAAAAAAAAA
1 AGAATTTAAAAAAAAA
1040651 AGAA-TTAAAAAAAAA
1 AGAATTTAAAAAAAAA
1040666 TTGGTGAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.16
Consensus pattern (16 bp):
AGAATTTAAAAAAAAA
Found at i:1041196 original size:8 final size:8
Alignment explanation
Indices: 1041158--1041199 Score: 57
Period size: 8 Copynumber: 5.1 Consensus size: 8
1041148 TTTTTGAAAA
*
1041158 AATTTAAT
1 AATTTTAT
1041166 AATTTATAT
1 AATTT-TAT
*
1041175 AACTTTAT
1 AATTTTAT
1041183 AATTTTAT
1 AATTTTAT
1041191 AATTTTAT
1 AATTTTAT
1041199 A
1 A
1041200 CCAATTCCCT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
8 24 0.80
9 6 0.20
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (8 bp):
AATTTTAT
Found at i:1043846 original size:173 final size:173
Alignment explanation
Indices: 1043557--1043902 Score: 629
Period size: 173 Copynumber: 2.0 Consensus size: 173
1043547 CACGTTTGAA
*
1043557 TTCATATCATTCTAATTGTTGCTAGAACAACGGTGCCAATTGCGTTAAGGCTTAATATATAGTAT
1 TTCATATCATTCTAATTGTTGCTAGAACAACGGTGCCAACTGCGTTAAGGCTTAATATATAGTAT
* * *
1043622 TTGGATGCGGAAATTGAGGGCATCGCTTTATGCAGTGATTTCCAAATTACAACATTGTAAGATGA
66 TAGGATGCGAAAATTGAGGGCATCGCTTTATGCAATGATTTCCAAATTACAACATTGTAAGATGA
*
1043687 ATCTTTCCATGACGAGGGCAACACTTAGGGGAGAGCAAATTTC
131 ATCTTTCCATGACAAGGGCAACACTTAGGGGAGAGCAAATTTC
1043730 TTCATATCATTCTAATTGTTGCTAGAACAACGGTGCCAACTGCGTTAAGGCTTAATATATAGTAT
1 TTCATATCATTCTAATTGTTGCTAGAACAACGGTGCCAACTGCGTTAAGGCTTAATATATAGTAT
* *
1043795 TAGGATGTGAAAATTGAGGGCATCGCTTTATGCAATGATTTCCAAATTACAACATTGTAAGATGG
66 TAGGATGCGAAAATTGAGGGCATCGCTTTATGCAATGATTTCCAAATTACAACATTGTAAGATGA
1043860 ATCTTTCCATGACAAGGGCAACACTTAGGGGAGAGCAAATTTC
131 ATCTTTCCATGACAAGGGCAACACTTAGGGGAGAGCAAATTTC
1043903 GGTTAAAACT
Statistics
Matches: 166, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
173 166 1.00
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Consensus pattern (173 bp):
TTCATATCATTCTAATTGTTGCTAGAACAACGGTGCCAACTGCGTTAAGGCTTAATATATAGTAT
TAGGATGCGAAAATTGAGGGCATCGCTTTATGCAATGATTTCCAAATTACAACATTGTAAGATGA
ATCTTTCCATGACAAGGGCAACACTTAGGGGAGAGCAAATTTC
Found at i:1053408 original size:31 final size:31
Alignment explanation
Indices: 1053334--1053412 Score: 108
Period size: 31 Copynumber: 2.6 Consensus size: 31
1053324 CGGGTGACCA
*
1053334 ATTTGTCACTTTCCGAAAACATTAGTTACTG
1 ATTTGTCACTTTTCGAAAACATTAGTTACTG
* *
1053365 ATTTGTCGCTTTTCGTAAACATTA-TTGACTG
1 ATTTGTCACTTTTCGAAAACATTAGTT-ACTG
1053396 ATTTGTCACTTTT-GAAA
1 ATTTGTCACTTTTCGAAA
1053413 GTTTAGTGAC
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
30 5 0.12
31 37 0.88
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (31 bp):
ATTTGTCACTTTTCGAAAACATTAGTTACTG
Found at i:1059831 original size:6 final size:6
Alignment explanation
Indices: 1059820--1059847 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
1059810 TAGGGAAACT
1059820 ATGCCC ATGCCC ATGCCC ATGCCC ATGC
1 ATGCCC ATGCCC ATGCCC ATGCCC ATGC
1059848 TATATATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.46, G:0.18, T:0.18
Consensus pattern (6 bp):
ATGCCC
Found at i:1062787 original size:35 final size:33
Alignment explanation
Indices: 1062740--1062809 Score: 88
Period size: 35 Copynumber: 2.1 Consensus size: 33
1062730 GTGATAATTG
1062740 GACACATGTTTTGTATTAACTTAATTACA-ACAT
1 GACACATGTTTTGTATTAACTTAATTA-AGACAT
* *
1062773 GACACAATGGTTTTGTGTTAAGTTAATTAAGACAT
1 GACAC-AT-GTTTTGTATTAACTTAATTAAGACAT
1062808 GA
1 GA
1062810 TTTGACATTG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
33 5 0.16
34 3 0.09
35 24 0.75
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.37
Consensus pattern (33 bp):
GACACATGTTTTGTATTAACTTAATTAAGACAT
Found at i:1063826 original size:2 final size:2
Alignment explanation
Indices: 1063821--1063856 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1063811 TTCACACACT
*
1063821 GA GA GA GA GA CA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1063857 AGGGGGGGGC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1066082 original size:7 final size:8
Alignment explanation
Indices: 1066063--1066087 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1066053 CAAATAATAC
1066063 AAAAAATT
1 AAAAAATT
1066071 AAAAAATT
1 AAAAAATT
1066079 AAAAAATT
1 AAAAAATT
1066087 A
1 A
1066088 TCAAAATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AAAAAATT
Found at i:1066188 original size:27 final size:27
Alignment explanation
Indices: 1066149--1066216 Score: 91
Period size: 27 Copynumber: 2.5 Consensus size: 27
1066139 CGAGGGACTA
* * *
1066149 CCACAGACGGCACTAAAGGTGCCAGTG
1 CCACAGGCGGCACCAAAGGTGCCACTG
* *
1066176 GCAGAGGCGGCACCAAAGGTGCCACTG
1 CCACAGGCGGCACCAAAGGTGCCACTG
1066203 CCACAGGCGGCACC
1 CCACAGGCGGCACC
1066217 CCCCTTATAT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.26, C:0.34, G:0.32, T:0.07
Consensus pattern (27 bp):
CCACAGGCGGCACCAAAGGTGCCACTG
Found at i:1068145 original size:3 final size:3
Alignment explanation
Indices: 1068139--1068177 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
1068129 AAGGAAAAAA
* *
1068139 AAG AAG AAG AAG -AG AAG AAG AAG ATG ATG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1068178 GAGATAACAG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.62, C:0.00, G:0.33, T:0.05
Consensus pattern (3 bp):
AAG
Found at i:1068156 original size:11 final size:11
Alignment explanation
Indices: 1068140--1068174 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
1068130 AGGAAAAAAA
1068140 AGAAGAAGAAG
1 AGAAGAAGAAG
1068151 AGAAGAAGAAG
1 AGAAGAAGAAG
*
1068162 ATGATGAAGAAG
1 A-GAAGAAGAAG
1068174 A
1 A
1068175 AGAGAGATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.60, C:0.00, G:0.34, T:0.06
Consensus pattern (11 bp):
AGAAGAAGAAG
Found at i:1068194 original size:23 final size:21
Alignment explanation
Indices: 1068168--1068219 Score: 59
Period size: 23 Copynumber: 2.4 Consensus size: 21
1068158 GAAGATGATG
1068168 AAGAAGAAGAGAGATAACAGAAA
1 AAGAAGAAGAGAGATAA-AG-AA
* *
1068191 AAGAATAATAGAGATAAAGAA
1 AAGAAGAAGAGAGATAAAGAA
*
1068212 CAGAAGAA
1 AAGAAGAA
1068220 AACAGGAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 8 0.32
22 2 0.08
23 15 0.60
ACGTcount: A:0.65, C:0.04, G:0.23, T:0.08
Consensus pattern (21 bp):
AAGAAGAAGAGAGATAAAGAA
Found at i:1068521 original size:14 final size:14
Alignment explanation
Indices: 1068504--1068536 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1068494 AATATATACA
1068504 TATATGTATGTGTG
1 TATATGTATGTGTG
*
1068518 TATATGTGTGTGTG
1 TATATGTATGTGTG
1068532 TATAT
1 TATAT
1068537 ATATAAACAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.21, C:0.00, G:0.27, T:0.52
Consensus pattern (14 bp):
TATATGTATGTGTG
Found at i:1069088 original size:15 final size:15
Alignment explanation
Indices: 1069068--1069096 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1069058 GCTTCTTTTA
1069068 ACCATCATCATCATC
1 ACCATCATCATCATC
1069083 ACCATCATCATCAT
1 ACCATCATCATCAT
1069097 ACTCAAGATC
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:0.34, C:0.38, G:0.00, T:0.28
Consensus pattern (15 bp):
ACCATCATCATCATC
Found at i:1078595 original size:28 final size:29
Alignment explanation
Indices: 1078555--1078609 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
1078545 TAAATATATA
1078555 TTTTTTAATTTTTTTAATTTTAAAATACT
1 TTTTTTAATTTTTTTAATTTTAAAATACT
* *
1078584 TTTTTTTA-TTTTTTATTTTTAAAATA
1 TTTTTTAATTTTTTTAATTTTAAAATA
1078610 AATTTTTGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 17 0.71
29 7 0.29
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (29 bp):
TTTTTTAATTTTTTTAATTTTAAAATACT
Found at i:1078615 original size:29 final size:30
Alignment explanation
Indices: 1078546--1078616 Score: 83
Period size: 28 Copynumber: 2.4 Consensus size: 30
1078536 CGAATATAAT
*
1078546 AAATATATATTTTTTAATTTTTTTAATTTTA
1 AAATAAAT-TTTTTTAATTTTTTTAATTTTA
* * *
1078577 AAAT-ACTTTTTTTTA-TTTTTTATTTTTA
1 AAATAAATTTTTTTAATTTTTTTAATTTTA
1078605 AAATAAATTTTT
1 AAATAAATTTTT
1078617 GGTGTTTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
28 16 0.47
29 13 0.38
30 1 0.03
31 4 0.12
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (30 bp):
AAATAAATTTTTTTAATTTTTTTAATTTTA
Found at i:1080658 original size:4 final size:4
Alignment explanation
Indices: 1080649--1080705 Score: 96
Period size: 4 Copynumber: 14.2 Consensus size: 4
1080639 ATTGAAAAGC
*
1080649 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA GGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
*
1080697 GGTA TGTA T
1 TGTA TGTA T
1080706 TTGTATATTT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 51 1.00
ACGTcount: A:0.25, C:0.00, G:0.28, T:0.47
Consensus pattern (4 bp):
TGTA
Found at i:1084700 original size:30 final size:30
Alignment explanation
Indices: 1084665--1084767 Score: 98
Period size: 31 Copynumber: 3.4 Consensus size: 30
1084655 TAACTAGGTC
*
1084665 CCTTCAAAATTTTTAAAAATTCTAAATAAA
1 CCTTCAAAATTTTTAAAAATTCTAATTAAA
* * *
1084695 CCTTCAAATAGTTTTAAAAATTTTAATTAGA
1 CCTTCAAA-ATTTTTAAAAATTCTAATTAAA
* * * * * *
1084726 CCCTCAAATTTTTTGAAAAGTCTCATTAAT
1 CCTTCAAAATTTTTAAAAATTCTAATTAAA
1084756 CCTCTCAAAATT
1 CCT-TCAAAATT
1084768 GTAACATTTT
Statistics
Matches: 56, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
30 24 0.43
31 32 0.57
ACGTcount: A:0.41, C:0.17, G:0.04, T:0.39
Consensus pattern (30 bp):
CCTTCAAAATTTTTAAAAATTCTAATTAAA
Found at i:1085113 original size:3 final size:3
Alignment explanation
Indices: 1085105--1085134 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
1085095 CAATGACCTG
*
1085105 CAA CAA CAA CAA CAA CAA CAA CAA GAA CAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
1085135 TTTCATGGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.67, C:0.30, G:0.03, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:1087806 original size:28 final size:28
Alignment explanation
Indices: 1087750--1087811 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
1087740 TGTATATATA
*
1087750 ATTATATATAATTATTTAAATATTATTT
1 ATTATATATAATTATTTAAAAATTATTT
* *
1087778 ATTATATTTAATTTTTTAAAAA-TA-TT
1 ATTATATATAATTATTTAAAAATTATTT
1087804 -TTATATAT
1 ATTATATAT
1087812 CATCAAATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
25 7 0.23
26 2 0.07
27 2 0.07
28 19 0.63
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (28 bp):
ATTATATATAATTATTTAAAAATTATTT
Found at i:1089269 original size:57 final size:58
Alignment explanation
Indices: 1089169--1089283 Score: 162
Period size: 57 Copynumber: 2.0 Consensus size: 58
1089159 ATAGAAATGG
* *
1089169 TGAAAATGGAGAAATGAGAAAATTTTGGAAATGATGATGATTTTCTCCAAAATGAAAA
1 TGAAAATGGAGAAATGAGAAAATTTTGGAAATGATGATAATTTTCTCCAAAAAGAAAA
* * *
1089227 TGAAAATGGAGAAATGA-AATCA-TTTGGAAATGATTATAATTTTCTCTAAAAAGAAAA
1 TGAAAATGGAGAAATGAGAA-AATTTTGGAAATGATGATAATTTTCTCCAAAAAGAAAA
1089284 AAATGAAAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
57 33 0.65
58 18 0.35
ACGTcount: A:0.48, C:0.05, G:0.18, T:0.29
Consensus pattern (58 bp):
TGAAAATGGAGAAATGAGAAAATTTTGGAAATGATGATAATTTTCTCCAAAAAGAAAA
Found at i:1090627 original size:16 final size:16
Alignment explanation
Indices: 1090606--1090636 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1090596 TGTGCAATTG
1090606 AATTTGATTCAATTTA
1 AATTTGATTCAATTTA
1090622 AATTTGATTCAATTT
1 AATTTGATTCAATTT
1090637 TCACAAACCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.52
Consensus pattern (16 bp):
AATTTGATTCAATTTA
Found at i:1094990 original size:26 final size:25
Alignment explanation
Indices: 1094926--1094976 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
1094916 AATGTGAAAA
1094926 TATGTCCTAAATTTCTTTTTTACTT
1 TATGTCCTAAATTTCTTTTTTACTT
1094951 TATGTCCTAAATTTCTTTTTTACTT
1 TATGTCCTAAATTTCTTTTTTACTT
1094976 T
1 T
1094977 CCAGTGTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.20, C:0.16, G:0.04, T:0.61
Consensus pattern (25 bp):
TATGTCCTAAATTTCTTTTTTACTT
Found at i:1097430 original size:60 final size:61
Alignment explanation
Indices: 1097357--1097471 Score: 146
Period size: 62 Copynumber: 1.9 Consensus size: 61
1097347 GAATTTGATA
* *
1097357 TTTTTTTTAAATTTGATA-TCTAAG-TTTTTTTGA-TCCAATTTGGTACTTGAACTTAATAT
1 TTTTTTTTAAATTTGATACT-TAAGTTTTTTTTAAGTCCAATTTGGTACTTAAACTTAATAT
* * *
1097416 TTTTTTTCTTAATTTGGTACTTAAGTTTTTTTTAAGTTCAATTTGGTACTTAAACT
1 TTTTTTT-TAAATTTGATACTTAAGTTTTTTTTAAGTCCAATTTGGTACTTAAACT
1097472 AATCACATGT
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
59 7 0.15
60 13 0.28
61 9 0.19
62 18 0.38
ACGTcount: A:0.25, C:0.09, G:0.10, T:0.56
Consensus pattern (61 bp):
TTTTTTTTAAATTTGATACTTAAGTTTTTTTTAAGTCCAATTTGGTACTTAAACTTAATAT
Found at i:1097445 original size:27 final size:29
Alignment explanation
Indices: 1097407--1097468 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
1097397 TGGTACTTGA
*
1097407 ACTTAATATTTTTTT-TCTT-AATTTGGT
1 ACTTAATATTTTTTTAACTTCAATTTGGT
*
1097434 ACTTAAGT-TTTTTTTAAGTTCAATTTGGT
1 ACTTAA-TATTTTTTTAACTTCAATTTGGT
1097463 ACTTAA
1 ACTTAA
1097469 ACTAATCACA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 13 0.43
28 3 0.10
29 14 0.47
ACGTcount: A:0.26, C:0.08, G:0.10, T:0.56
Consensus pattern (29 bp):
ACTTAATATTTTTTTAACTTCAATTTGGT
Found at i:1098809 original size:19 final size:17
Alignment explanation
Indices: 1098785--1098819 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
1098775 TTTTTTTGGA
1098785 TATTGTATAACTCTTGTTT
1 TATTGT-TAACT-TTGTTT
1098804 TATTGTTAACTTTGTT
1 TATTGTTAACTTTGTT
1098820 ACTATTTTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 5 0.31
19 6 0.38
ACGTcount: A:0.20, C:0.09, G:0.11, T:0.60
Consensus pattern (17 bp):
TATTGTTAACTTTGTTT
Found at i:1098825 original size:18 final size:19
Alignment explanation
Indices: 1098785--1098825 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
1098775 TTTTTTTGGA
*
1098785 TATTGTATAACTCTTGTTT
1 TATTGTATAACTCTTGTTC
1098804 TATTGT-TAACT-TTGTTAC
1 TATTGTATAACTCTTGTT-C
1098822 TATT
1 TATT
1098826 TTAGAGACAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 5 0.25
18 9 0.45
19 6 0.30
ACGTcount: A:0.22, C:0.10, G:0.10, T:0.59
Consensus pattern (19 bp):
TATTGTATAACTCTTGTTC
Found at i:1100188 original size:16 final size:17
Alignment explanation
Indices: 1100167--1100199 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1100157 AAATTTTATA
1100167 TAAATAT-TTATAATTT
1 TAAATATATTATAATTT
1100183 TAAATATGATTATAATT
1 TAAATAT-ATTATAATT
1100200 AGATGAGGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (17 bp):
TAAATATATTATAATTT
Found at i:1100749 original size:19 final size:21
Alignment explanation
Indices: 1100711--1100751 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 21
1100701 TCACTCTTAG
1100711 GATTCGAGGTTTGAGGTTCAA
1 GATTCGAGGTTTGAGGTTCAA
*
1100732 GATTC-AGGTTT-TGGTTCAA
1 GATTCGAGGTTTGAGGTTCAA
1100751 G
1 G
1100752 CTGATTCGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 8 0.42
20 6 0.32
21 5 0.26
ACGTcount: A:0.22, C:0.10, G:0.32, T:0.37
Consensus pattern (21 bp):
GATTCGAGGTTTGAGGTTCAA
Found at i:1103121 original size:21 final size:22
Alignment explanation
Indices: 1103097--1103157 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 22
1103087 AAATAGCAGC
* *
1103097 AAAATAGTAA-AAAATAATAAG
1 AAAATAGCAACAAAATAACAAG
1103118 AAAATAGCAACAAAATAACAAG
1 AAAATAGCAACAAAATAACAAG
* *
1103140 --AATAGGAAAAAAATAACA
1 AAAATAGCAACAAAATAACA
1103158 TTGTTTTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 16 0.46
21 9 0.26
22 10 0.29
ACGTcount: A:0.70, C:0.07, G:0.10, T:0.13
Consensus pattern (22 bp):
AAAATAGCAACAAAATAACAAG
Found at i:1108610 original size:7 final size:7
Alignment explanation
Indices: 1108595--1108624 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
1108585 AAAAATTAGA
1108595 TTAGGGT
1 TTAGGGT
*
1108602 TTAGTGT
1 TTAGGGT
1108609 TTAGGGT
1 TTAGGGT
1108616 TTAGGGT
1 TTAGGGT
1108623 TT
1 TT
1108625 TTAAGAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.13, C:0.00, G:0.37, T:0.50
Consensus pattern (7 bp):
TTAGGGT
Found at i:1108663 original size:104 final size:102
Alignment explanation
Indices: 1108417--1108884 Score: 623
Period size: 96 Copynumber: 4.8 Consensus size: 102
1108407 GTTTTTAGAT
* * * *
1108417 TTTAGGG-TTTTAAGGAAAAAATCAAATAAATTAGTGTTTAAGGTTTCTTGAGTAAATTAATTAT
1 TTTAGGGTTTTTAAGAAAAAAATCAAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTAT
1108481 AAATTTT-AAAAAATTAGATTAGGGTTTAGTGTTTA-
66 AAATTTTAAAAAAATTAGATTAGGGTTTAGTGTTTAG
1108516 ---A-GGTTTTTAAGAAAAAAAT-AAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTAT
1 TTTAGGGTTTTTAAGAAAAAAATCAAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTAT
1108576 AAATTTTAAAAAAATTAGATTAGGGTTTAGTGTTTAGGG
66 AAATTTTAAAAAAATTAGATTAGGGTTTAGTGTTTA--G
* *
1108615 TTTAGGGTTTTTAAGAAAAAAATTAAATAAATTAGGGTTTAGGATTACTTGAGTAAATTAATTAT
1 TTTAGGGTTTTTAAGAAAAAAATCAAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTAT
*
1108680 AAATTTTAAAAAATTTAGATTAGGGTTTA--G--T-G
66 AAATTTTAAAAAAATTAGATTAGGGTTTAGTGTTTAG
* * *
1108712 TTTAGGGTTTTTAAGGAAAAAATCAAATAAATTAGAGTTTGGGGTTACTTGAGTAAATTAATTAT
1 TTTAGGGTTTTTAAGAAAAAAATCAAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTAT
* *
1108777 AAATTTTAAAAAATTTAGATTAAGGTTTAGTGTTTAG
66 AAATTTTAAAAAAATTAGATTAGGGTTTAGTGTTTAG
* * * * *
1108814 ----GGG-TTTTAAG-GAAAAATCAAATAAATTAGGGTTTAGGGTTACTTAATTAAATTATTTGT
1 TTTAGGGTTTTTAAGAAAAAAATCAAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTAT
*
1108873 TAATTTTAAAAA
66 AAATTTTAAAAA
1108885 GCTCCTACGT
Statistics
Matches: 334, Mismatches: 20, Indels: 33
0.86 0.05 0.09
Matches are distributed among these distances:
95 47 0.14
96 96 0.29
97 96 0.29
98 3 0.01
99 1 0.00
100 1 0.00
101 1 0.00
102 3 0.01
103 18 0.05
104 68 0.20
ACGTcount: A:0.40, C:0.02, G:0.18, T:0.40
Consensus pattern (102 bp):
TTTAGGGTTTTTAAGAAAAAAATCAAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTAT
AAATTTTAAAAAAATTAGATTAGGGTTTAGTGTTTAG
Found at i:1108734 original size:97 final size:97
Alignment explanation
Indices: 1108417--1108884 Score: 683
Period size: 97 Copynumber: 4.8 Consensus size: 97
1108407 GTTTTTAGAT
* * *
1108417 TTTAGGG-TTTTAAGGAAAAAATCAAATAAATTAGTGTTTAAGGTTTCTTGAGTAAATTAATTAT
1 TTTAGGGTTTTTAAGGAAAAAATCAAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTAT
1108481 AAATTTTAAAAAA-TTAGATTAGGGTTTAGTG
66 AAATTTTAAAAAATTTAGATTAGGGTTTAGTG
* *
1108512 TTTAAGGTTTTTAAGAAAAAAAT-AAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTAT
1 TTTAGGGTTTTTAAGGAAAAAATCAAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTAT
*
1108576 AAATTTTAAAAAAATTAGATTAGGGTTTAGTGTTTAGGG
66 AAATTTTAAAAAATTTAGATTAGGGTTTA--G--T---G
* * *
1108615 TTTAGGGTTTTTAAGAAAAAAATTAAATAAATTAGGGTTTAGGATTACTTGAGTAAATTAATTAT
1 TTTAGGGTTTTTAAGGAAAAAATCAAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTAT
1108680 AAATTTTAAAAAATTTAGATTAGGGTTTAGTG
66 AAATTTTAAAAAATTTAGATTAGGGTTTAGTG
* *
1108712 TTTAGGGTTTTTAAGGAAAAAATCAAATAAATTAGAGTTTGGGGTTACTTGAGTAAATTAATTAT
1 TTTAGGGTTTTTAAGGAAAAAATCAAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTAT
*
1108777 AAATTTTAAAAAATTTAGATTAAGGTTTAGTG
66 AAATTTTAAAAAATTTAGATTAGGGTTTAGTG
* * * * *
1108809 TTTAGGGGTTTTAAGG-AAAAATCAAATAAATTAGGGTTTAGGGTTACTTAATTAAATTATTTGT
1 TTTAGGGTTTTTAAGGAAAAAATCAAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTAT
*
1108873 TAATTTTAAAAA
66 AAATTTTAAAAA
1108885 GCTCCTACGT
Statistics
Matches: 341, Mismatches: 22, Indels: 19
0.89 0.06 0.05
Matches are distributed among these distances:
95 57 0.17
96 82 0.24
97 107 0.31
98 1 0.00
100 2 0.01
102 1 0.00
103 23 0.07
104 68 0.20
ACGTcount: A:0.40, C:0.02, G:0.18, T:0.40
Consensus pattern (97 bp):
TTTAGGGTTTTTAAGGAAAAAATCAAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTAT
AAATTTTAAAAAATTTAGATTAGGGTTTAGTG
Found at i:1109108 original size:126 final size:126
Alignment explanation
Indices: 1108883--1109173 Score: 424
Period size: 126 Copynumber: 2.3 Consensus size: 126
1108873 TAATTTTAAA
* *
1108883 AAGCTCCTACGTGGACGCTCTTTTGCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGTTT
1 AAGCTCCCACGTGAACGCTCTTTTGCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGTTT
* * * **
1108948 CTGAGCAAATAGTGCAAAAAATGCTTTAAGCAGGATGCATTGTTTGCAAAAGTACTGAAAG
66 CTGAGCAAATAGTGCAAAAAACGCTTCAAGCAGGATGCAATGTCAGCAAAAGTACTGAAAG
* * * * *
1109009 AAGCTCTCACGTTGAA-GCTTTTTTGCTACAATAGTTTCTGAAAAAATAATTTTGAGAAGATGTT
1 AAGCTCCCACG-TGAACGCTCTTTTGCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGTT
* *
1109073 TCTGAGTAACTAGTGTC-AAAAACGCTTCAAGCAGGATGCAATGTCAGCAAAAGTACTGAAAG
65 TCTGAGCAAATAGTG-CAAAAAACGCTTCAAGCAGGATGCAATGTCAGCAAAAGTACTGAAAG
1109135 AAGCTCCCACGTGAACGCTCTTTTGCTACAGTAGTTCCT
1 AAGCTCCCACGTGAACGCTCTTTTGCTACAGTAGTTCCT
1109174 ATTTGGCCTG
Statistics
Matches: 144, Mismatches: 18, Indels: 6
0.86 0.11 0.04
Matches are distributed among these distances:
125 4 0.03
126 136 0.94
127 4 0.03
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (126 bp):
AAGCTCCCACGTGAACGCTCTTTTGCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGTTT
CTGAGCAAATAGTGCAAAAAACGCTTCAAGCAGGATGCAATGTCAGCAAAAGTACTGAAAG
Found at i:1110073 original size:7 final size:7
Alignment explanation
Indices: 1110063--1110088 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1110053 TTATATACAT
1110063 AATACTA
1 AATACTA
1110070 AATACTA
1 AATACTA
1110077 AATACTA
1 AATACTA
1110084 AATAC
1 AATAC
1110089 GAATCGACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (7 bp):
AATACTA
Found at i:1114110 original size:13 final size:13
Alignment explanation
Indices: 1114088--1114117 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1114078 AGCCCAAACT
*
1114088 CAATTGCCCAACC
1 CAATTACCCAACC
1114101 CAATTACCCAACC
1 CAATTACCCAACC
1114114 CAAT
1 CAAT
1114118 AAAACTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.43, G:0.03, T:0.17
Consensus pattern (13 bp):
CAATTACCCAACC
Found at i:1114268 original size:9 final size:9
Alignment explanation
Indices: 1114256--1114314 Score: 75
Period size: 9 Copynumber: 6.4 Consensus size: 9
1114246 AAAATAAAAA
1114256 AATTCGGGT
1 AATTCGGGT
1114265 AATTCGGGT
1 AATTCGGGT
*
1114274 ATTTTTC-GGT
1 A--ATTCGGGT
*
1114284 AATTCGGTT
1 AATTCGGGT
1114293 AATTCGGGT
1 AATTCGGGT
1114302 AATTCGGGT
1 AATTCGGGT
1114311 AATT
1 AATT
1114315 TTTAACCAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
8 3 0.07
9 33 0.77
10 4 0.09
11 3 0.07
ACGTcount: A:0.22, C:0.10, G:0.27, T:0.41
Consensus pattern (9 bp):
AATTCGGGT
Found at i:1118536 original size:162 final size:162
Alignment explanation
Indices: 1118351--1118715 Score: 522
Period size: 162 Copynumber: 2.3 Consensus size: 162
1118341 AAGGTGAAGA
* ** *
1118351 AAATGGTGAAGATGCATATTTTGATGATTGGAGGTCTAAGCTTAGTA-GCAACCAAGGATTTGTT
1 AAATGGTGAAGATGAATATTTTGATGATTGGAGGTCTAAGCTTAG-AGGCAACCAAGGAAATGGT
* *
1118415 GAAGAT-AATTATGTTGATGATTGGAGGTCTAAGCTTAGTAGCAACCATGGAAATGAAGAATTTG
65 GAAGATGAA-TATGTTGATGACTGGAGGTCTAAGCTTAGTAGCAACCATGGAAAGGAAGAATTTG
*
1118479 ATGATTGG-GACCATGATTTTAGTGGCAGCCATGG
129 ATGATTGGAG-CCATGATTTTAGTGGCAGCCAGGG
** *
1118513 AAATGGTGAAGATTTATATTTTGATGATTGGAGGTCTAAGCTTAGAGGCAACCATGGAAATGGTG
1 AAATGGTGAAGATGAATATTTTGATGATTGGAGGTCTAAGCTTAGAGGCAACCAAGGAAATGGTG
* * * *
1118578 AAGATGCATATTTTGATGACTGGAGGTCTAAGCTTAGTGGCAACCATGGAGAGGAAGAATTTGAT
66 AAGATGAATATGTTGATGACTGGAGGTCTAAGCTTAGTAGCAACCATGGAAAGGAAGAATTTGAT
1118643 GATTGGAGCCATGATTTTAGTGGCAGCCAGGG
131 GATTGGAGCCATGATTTTAGTGGCAGCCAGGG
* *
1118675 AAATAGTGAAGATGAATATTTTGAT-ACTTGGAGATCTAAGC
1 AAATGGTGAAGATGAATATTTTGATGA-TTGGAGGTCTAAGC
1118716 CCAGTTCCAA
Statistics
Matches: 182, Mismatches: 17, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
161 2 0.01
162 178 0.98
163 2 0.01
ACGTcount: A:0.32, C:0.10, G:0.28, T:0.30
Consensus pattern (162 bp):
AAATGGTGAAGATGAATATTTTGATGATTGGAGGTCTAAGCTTAGAGGCAACCAAGGAAATGGTG
AAGATGAATATGTTGATGACTGGAGGTCTAAGCTTAGTAGCAACCATGGAAAGGAAGAATTTGAT
GATTGGAGCCATGATTTTAGTGGCAGCCAGGG
Found at i:1118543 original size:57 final size:56
Alignment explanation
Indices: 1118475--1118715 Score: 180
Period size: 57 Copynumber: 4.4 Consensus size: 56
1118465 AAATGAAGAA
* ** * *
1118475 TTTGATGATTGG-GACCATGATTTTAGTGGCAGCCATGGAAATGGTGAAGATTTATAT
1 TTTGATGATTGGAGACC-TAAGCTTAGTGGCAACCATGGAAATGGTGAAGA-TGATAT
** *
1118532 TTTGATGATTGGAGGTCTAAGCTTAGAGGCAACCATGGAAATGGTGAAGATGCATAT
1 TTTGATGATTGGAGACCTAAGCTTAGTGGCAACCATGGAAATGGTGAAGATG-ATAT
* ** *
1118589 TTTGATGACTGGAGGTCTAAGCTTAGTGGCAACCATGGAGA--G-G-A-A-GA-A-
1 TTTGATGATTGGAGACCTAAGCTTAGTGGCAACCATGGAAATGGTGAAGATGATAT
* ** * * *
1118637 TTTGATGATTGGAG-CCATGATTTTAGTGGCAGCCAGGGAAATAGTGAAGATGAATAT
1 TTTGATGATTGGAGACC-TAAGCTTAGTGGCAACCATGGAAATGGTGAAGATG-ATAT
*
1118694 TTTGAT-ACTTGGAGATCTAAGC
1 TTTGATGA-TTGGAGACCTAAGC
1118716 CCAGTTCCAA
Statistics
Matches: 147, Mismatches: 23, Indels: 28
0.74 0.12 0.14
Matches are distributed among these distances:
47 1 0.01
48 31 0.21
49 1 0.01
50 2 0.01
51 2 0.01
52 2 0.01
53 2 0.01
54 2 0.01
55 2 0.01
56 3 0.02
57 96 0.65
58 3 0.02
ACGTcount: A:0.30, C:0.10, G:0.29, T:0.30
Consensus pattern (56 bp):
TTTGATGATTGGAGACCTAAGCTTAGTGGCAACCATGGAAATGGTGAAGATGATAT
Found at i:1118641 original size:105 final size:105
Alignment explanation
Indices: 1118532--1118750 Score: 253
Period size: 105 Copynumber: 2.1 Consensus size: 105
1118522 AGATTTATAT
* * * *
1118532 TTTGATGATTGGAGGTC-TAAGCTTAGAGGCAACCATGGAAATGGTGAAGATGCATATTTTGATG
1 TTTGATGATTGGA-GCCATAAGCTTAGAGGCAACCAGGGAAATAGTGAAGATGAATATTTTGAT-
* ** * * * *
1118596 AC-TGGAGGTCTAAGCTTAGTGGCAACCATGGAGAGGAAGAA
64 ACTTGGAGATCTAAGCCCAGTGCCAACAATGGAAACGAAGAA
* ** * *
1118637 TTTGATGATTGGAGCCATGATTTTAGTGGCAGCCAGGGAAATAGTGAAGATGAATATTTTGATAC
1 TTTGATGATTGGAGCCATAAGCTTAGAGGCAACCAGGGAAATAGTGAAGATGAATATTTTGATAC
*
1118702 TTGGAGATCTAAGCCCAGTTCCAACAATGGAAACGAAGAA
66 TTGGAGATCTAAGCCCAGTGCCAACAATGGAAACGAAGAA
1118742 TTTGATGAT
1 TTTGATGAT
1118751 CGGGACCATG
Statistics
Matches: 95, Mismatches: 17, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
104 4 0.04
105 91 0.96
ACGTcount: A:0.32, C:0.12, G:0.28, T:0.27
Consensus pattern (105 bp):
TTTGATGATTGGAGCCATAAGCTTAGAGGCAACCAGGGAAATAGTGAAGATGAATATTTTGATAC
TTGGAGATCTAAGCCCAGTGCCAACAATGGAAACGAAGAA
Found at i:1118760 original size:105 final size:105
Alignment explanation
Indices: 1118554--1118769 Score: 274
Period size: 105 Copynumber: 2.1 Consensus size: 105
1118544 AGGTCTAAGC
* * * * * ** *
1118554 TTAGAGGCAACCATGGAAATGGTGAAGATGCATATTTTGATGACTGGAGGTCTAAGCTTAGTGGC
1 TTAGTGGCAACCAGGGAAATAGTGAAGATGAATATTTTGATGACTGGAGATCTAAGCCCAGTGCC
* * * *
1118619 AACCATGGAGAGGAAGAATTTGATGATTGGAGCCATGATT
66 AACAATGGAAACGAAGAATTTGATGATGGGAGCCATGATT
* *
1118659 TTAGTGGCAGCCAGGGAAATAGTGAAGATGAATATTTTGAT-ACTTGGAGATCTAAGCCCAGTTC
1 TTAGTGGCAACCAGGGAAATAGTGAAGATGAATATTTTGATGAC-TGGAGATCTAAGCCCAGTGC
1118723 CAACAATGGAAACGAAGAATTTGATGATCGGGA-CCATGATT
65 CAACAATGGAAACGAAGAATTTGATGAT-GGGAGCCATGATT
1118764 TTAGTG
1 TTAGTG
1118770 CCCGTCATGG
Statistics
Matches: 95, Mismatches: 14, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
104 2 0.02
105 90 0.95
106 3 0.03
ACGTcount: A:0.32, C:0.12, G:0.28, T:0.27
Consensus pattern (105 bp):
TTAGTGGCAACCAGGGAAATAGTGAAGATGAATATTTTGATGACTGGAGATCTAAGCCCAGTGCC
AACAATGGAAACGAAGAATTTGATGATGGGAGCCATGATT
Found at i:1125660 original size:206 final size:206
Alignment explanation
Indices: 1125306--1125714 Score: 746
Period size: 206 Copynumber: 2.0 Consensus size: 206
1125296 TATGTTAATG
* * *
1125306 TTTAGGTTTTTGAGAACAGAACTCAACTGTTTAAGCCAAATTAACTAAACTTTAACATTTAAAAT
1 TTTAGGTTTTCGAGAACAAAACTCAACTGTTTAAGCCAAATTAACTAAACTTGAACATTTAAAAT
1125371 TTGGGTTTAAATGTTTTCAGACTATTCAGGTAATGGTACTGGACCATCTAAGGAATTTAGTGCTC
66 TTGGGTTTAAATGTTTTCAGACTATTCAGGTAATGGTACTGGACCATCTAAGGAATTTAGTGCTC
1125436 CAACCTCTCTAGGAGCCTACCAGGCTGGAAGTTATGGAAATGAACAATCAATCCAAGGTAAATCA
131 CAACCTCTCTAGGAGCCTACCAGGCTGGAAGTTATGGAAATGAACAATCAATCCAAGGTAAATCA
1125501 TTTGATTTTCT
196 TTTGATTTTCT
* ** * *
1125512 TTTAGGTTTTCGAGAATAAAACTCAGTTGTTTAAGCCAAATTAACTAAGCTTGAACTTTTAAAAT
1 TTTAGGTTTTCGAGAACAAAACTCAACTGTTTAAGCCAAATTAACTAAACTTGAACATTTAAAAT
1125577 TTGGGTTTAAATGTTTTCAGACTATTCAGGTAATGGTACTGGACCATCTAAGGAATTTAGTGCTC
66 TTGGGTTTAAATGTTTTCAGACTATTCAGGTAATGGTACTGGACCATCTAAGGAATTTAGTGCTC
1125642 CAACCTCTCTAGGAGCCTACCAGGCTGGAAGTTATGGAAATGAACAATCAATCCAAGGTAAATCA
131 CAACCTCTCTAGGAGCCTACCAGGCTGGAAGTTATGGAAATGAACAATCAATCCAAGGTAAATCA
1125707 TTTGATTT
196 TTTGATTT
1125715 CTATTATATG
Statistics
Matches: 195, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
206 195 1.00
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (206 bp):
TTTAGGTTTTCGAGAACAAAACTCAACTGTTTAAGCCAAATTAACTAAACTTGAACATTTAAAAT
TTGGGTTTAAATGTTTTCAGACTATTCAGGTAATGGTACTGGACCATCTAAGGAATTTAGTGCTC
CAACCTCTCTAGGAGCCTACCAGGCTGGAAGTTATGGAAATGAACAATCAATCCAAGGTAAATCA
TTTGATTTTCT
Found at i:1125912 original size:230 final size:227
Alignment explanation
Indices: 1125512--1126166 Score: 963
Period size: 230 Copynumber: 2.9 Consensus size: 227
1125502 TTGATTTTCT
* * * *
1125512 TTTAGGTTTTCGAGAATAAAACTCAGTTGTTTAAGCCAAATTAACTAAGCTTGAACTTTTAAAAT
1 TTTAGGTTTTCGAGAATAAAACTCAATTG-TTAAGCCAAATTAACTAAGCTTTAACATTTAAATT
* *
1125577 TTGGGTTTAAATGTTTTCAGACTATTCAGGTAATGGTACTGGACCATCTAAGGAATTTAGTGCTC
65 TTGGGTCTAAATGTTTTCAGACTATTCAGGTAATAGTACTGGACCATCTAAGGAATTTAGTGCTC
* *
1125642 CAACCTCTCTAGGAGCCTACCAGGCTGGAAGTTATGGAAATGAACAATCAATCCAAGGTAAATCA
130 CAAGCTCTCTAGGTGCCTACCAGGCTGGAAGTTATGGAAATGAACAATCAATCCAAGGTAAATCA
* *
1125707 TTTGATTTCTATTATATG-TATATATGTTAATG
195 TTTGATTTCCATTACATGATATATATGTTAATG
* * *
1125739 TTTAGGTTTTCGAGAATAAAACTCAATTGTTCGAGCCAAATTAACAAAGTTTTAACATTTAAATT
1 TTTAGGTTTTCGAGAATAAAACTCAATTGTT-AAGCCAAATTAACTAAGCTTTAACATTTAAATT
*
1125804 TTGGGTCTAAATGTTTTGATCAGACTATTCAGGTAATAATACTGGACCATCTAAGGAATTTAGTG
65 TTGGGTCTAAATG-TTT--TCAGACTATTCAGGTAATAGTACTGGACCATCTAAGGAATTTAGTG
1125869 CTCCAAGCTCTCTAGGTGCCTACCAGGCTGGAAGTTATGGAAATGAACAATCAATCCAAGGTAAA
127 CTCCAAGCTCTCTAGGTGCCTACCAGGCTGGAAGTTATGGAAATGAACAATCAATCCAAGGTAAA
*
1125934 TCGTTTGATTTCCATTACATGTATATATATGTTAATG
192 TCATTTGATTTCCATTACATG-ATATATATGTTAATG
* * ** *
1125971 TTTAGATTTTCGAAAATAAAACTCAACCGTATAAGCTAAATTAACTAAGCTTTAACA-TTAAATT
1 TTTAGGTTTTCGAGAATAAAACTCAATTGT-TAAGCCAAATTAACTAAGCTTTAACATTTAAATT
* ** * *
1126035 TTGGGTCTAAATGTTTTCAGGCTATTCAGGTAATAGTACTACACCATCTAAAGAATTTAGTACTC
65 TTGGGTCTAAATGTTTTCAGACTATTCAGGTAATAGTACTGGACCATCTAAGGAATTTAGTGCTC
* * * * *
1126100 CAAGCTCTCTAGGTACCTACCAAGCCGGAAGTTATGGAAATAAACAATCAATCCCAGGTAAATCA
130 CAAGCTCTCTAGGTGCCTACCAGGCTGGAAGTTATGGAAATGAACAATCAATCCAAGGTAAATCA
1126165 TT
195 TT
1126167 ATGCCTACAT
Statistics
Matches: 386, Mismatches: 35, Indels: 13
0.89 0.08 0.03
Matches are distributed among these distances:
226 2 0.01
227 67 0.17
228 107 0.28
230 128 0.33
231 20 0.05
232 61 0.16
233 1 0.00
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (227 bp):
TTTAGGTTTTCGAGAATAAAACTCAATTGTTAAGCCAAATTAACTAAGCTTTAACATTTAAATTT
TGGGTCTAAATGTTTTCAGACTATTCAGGTAATAGTACTGGACCATCTAAGGAATTTAGTGCTCC
AAGCTCTCTAGGTGCCTACCAGGCTGGAAGTTATGGAAATGAACAATCAATCCAAGGTAAATCAT
TTGATTTCCATTACATGATATATATGTTAATG
Found at i:1127116 original size:2 final size:2
Alignment explanation
Indices: 1127109--1127151 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1127099 AAGAAGCTTT
1127109 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1127151 T
1 T
1127152 GAATAAGGAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1137552 original size:23 final size:22
Alignment explanation
Indices: 1137512--1137555 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
1137502 ATTTTTACTA
1137512 ATTATAAATTTATGATTTATAC
1 ATTATAAATTTATGATTTATAC
1137534 ATTATAAAATATTAT-ATTTATA
1 ATTAT-AAAT-TTATGATTTATA
1137556 TTTTTTTTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 5 0.25
23 11 0.55
24 4 0.20
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (22 bp):
ATTATAAATTTATGATTTATAC
Found at i:1154732 original size:93 final size:93
Alignment explanation
Indices: 1154545--1154745 Score: 217
Period size: 93 Copynumber: 2.2 Consensus size: 93
1154535 GGTTCTGACC
* * ** *
1154545 ACCGAATCGTTGGTTTTAGTAACAGGATTGGGTGCTAAAGCAGGGGACATTGCCGGAGCTGGTGA
1 ACCGAATCATTGGTTTTAGTAACAGGATTGGGTGCTAAAGCAGGGGACATAGCCGGAGCCAGCGA
*** ** *
1154610 AGATTTGCTTTCTTCACCGGATTTAACA
66 AGAACCGAATCCTTCACCGGATTTAACA
* *
1154638 ACCGAATCATTGGTTTTAGTAACCGGATTGGGTGCTACAA-CAGGGGACATAGCTGGAGCCAGCG
1 ACCGAATCATTGGTTTTAGTAACAGGATTGGGTGCTA-AAGCAGGGGACATAGCCGGAGCCAGCG
* * *
1154702 AAGAAACCGAATCCTT-ACTGGTTTTTACA
65 AAG-AACCGAATCCTTCACCGGATTTAACA
*
1154731 ACAGAATCATTGGTT
1 ACCGAATCATTGGTT
1154746 GCTAAAACAG
Statistics
Matches: 89, Mismatches: 17, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
93 81 0.91
94 8 0.09
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.27
Consensus pattern (93 bp):
ACCGAATCATTGGTTTTAGTAACAGGATTGGGTGCTAAAGCAGGGGACATAGCCGGAGCCAGCGA
AGAACCGAATCCTTCACCGGATTTAACA
Found at i:1154755 original size:75 final size:75
Alignment explanation
Indices: 1154664--1154895 Score: 313
Period size: 75 Copynumber: 3.1 Consensus size: 75
1154654 TAGTAACCGG
* * * * * * * *
1154664 ATTGGGTGCTACAACA-GGGGACATAGCTGGAGCCAGCGAAGAAACCGAATCCTTACTGGTTTTT
1 ATTGGTTGCTAAAACAGGGGGA-ATTGCCGGAGCCGGCGAAGAAACAGAATCCTCACCGGTTTTT
*
1154728 ACAACAGAATC
65 ACAACGGAATC
1154739 ATTGGTTGCTAAAACAGGGGGAATTGCCGGAGCCGGCGAAGAAACAGAATCCTCACCGGTTTTTA
1 ATTGGTTGCTAAAACAGGGGGAATTGCCGGAGCCGGCGAAGAAACAGAATCCTCACCGGTTTTTA
1154804 CAACGGAATC
66 CAACGGAATC
** * *
1154814 ATTGGTTGCTAATGCAGGGGGAATTGCCGGAGCCGGCGAAGAAATAGAATCCTCACCGGTTTTAA
1 ATTGGTTGCTAAAACAGGGGGAATTGCCGGAGCCGGCGAAGAAACAGAATCCTCACCGGTTTTTA
*
1154879 CAATGGAATC
66 CAACGGAATC
*
1154889 ATCGGTT
1 ATTGGTT
1154896 TCAGTAATGG
Statistics
Matches: 141, Mismatches: 15, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
75 136 0.96
76 5 0.04
ACGTcount: A:0.30, C:0.20, G:0.28, T:0.22
Consensus pattern (75 bp):
ATTGGTTGCTAAAACAGGGGGAATTGCCGGAGCCGGCGAAGAAACAGAATCCTCACCGGTTTTTA
CAACGGAATC
Found at i:1161483 original size:2 final size:2
Alignment explanation
Indices: 1161476--1161507 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1161466 AATTTAGCCC
1161476 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1161508 TTGTAAATGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1163912 original size:20 final size:21
Alignment explanation
Indices: 1163887--1163935 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
1163877 GCTTGGCTCG
1163887 GATACCCTTAAC-AAAGTATC
1 GATACCCTTAACAAAAGTATC
* **
1163907 GATACCTTTTTCAAAAGTATC
1 GATACCCTTAACAAAAGTATC
*
1163928 GACACCCT
1 GATACCCT
1163936 GCTTGAGAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.35, C:0.27, G:0.10, T:0.29
Consensus pattern (21 bp):
GATACCCTTAACAAAAGTATC
Found at i:1166091 original size:29 final size:29
Alignment explanation
Indices: 1166049--1166115 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
1166039 ATAGGGATTT
*
1166049 GATCAAATTAGT-CCTTCAACTATTAAATA
1 GATCAAATTAGTCCCTT-AACTATTAAAAA
* *
1166078 GATCAATTTAGTCCCTTTACTATTAAAAA
1 GATCAAATTAGTCCCTTAACTATTAAAAA
1166107 GAATCAAAT
1 G-ATCAAAT
1166116 AAGACCAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 22 0.69
30 10 0.31
ACGTcount: A:0.42, C:0.16, G:0.07, T:0.34
Consensus pattern (29 bp):
GATCAAATTAGTCCCTTAACTATTAAAAA
Found at i:1166236 original size:53 final size:53
Alignment explanation
Indices: 1166178--1166283 Score: 212
Period size: 53 Copynumber: 2.0 Consensus size: 53
1166168 ATTGAAAAAT
1166178 AATAACTTTCAATACATTTTTTAGATAGTGAATGTTAACTCTATTACAATTTG
1 AATAACTTTCAATACATTTTTTAGATAGTGAATGTTAACTCTATTACAATTTG
1166231 AATAACTTTCAATACATTTTTTAGATAGTGAATGTTAACTCTATTACAATTTG
1 AATAACTTTCAATACATTTTTTAGATAGTGAATGTTAACTCTATTACAATTTG
1166284 GACTTATTTA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.36, C:0.11, G:0.09, T:0.43
Consensus pattern (53 bp):
AATAACTTTCAATACATTTTTTAGATAGTGAATGTTAACTCTATTACAATTTG
Found at i:1174188 original size:7 final size:7
Alignment explanation
Indices: 1174178--1174205 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
1174168 AAATGGAAAA
1174178 TTGGGTG
1 TTGGGTG
1174185 TTGGGTG
1 TTGGGTG
1174192 TTGGGTG
1 TTGGGTG
1174199 TTGGGTG
1 TTGGGTG
1174206 GATTCTTGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.00, C:0.00, G:0.57, T:0.43
Consensus pattern (7 bp):
TTGGGTG
Found at i:1176141 original size:4 final size:4
Alignment explanation
Indices: 1176126--1176161 Score: 58
Period size: 4 Copynumber: 9.5 Consensus size: 4
1176116 TTTTTGTGTC
1176126 TAAT TAA- T-AT TAAT TAAT TAAT TAAT TAAT TAAT TA
1 TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TA
1176162 TAAGCTTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 1 0.03
3 2 0.07
4 27 0.90
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
TAAT
Found at i:1176680 original size:10 final size:10
Alignment explanation
Indices: 1176665--1176691 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
1176655 CAATGTCAAG
1176665 GGGGCAAGTA
1 GGGGCAAGTA
1176675 GGGGCAAGTA
1 GGGGCAAGTA
1176685 GGGGCAA
1 GGGGCAA
1176692 TCTTGTTAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.30, C:0.11, G:0.52, T:0.07
Consensus pattern (10 bp):
GGGGCAAGTA
Found at i:1178938 original size:16 final size:17
Alignment explanation
Indices: 1178913--1178945 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1178903 GTAATTTTAC
*
1178913 TTTTATAAA-TTTAAAA
1 TTTTAAAAATTTTAAAA
1178929 TTTTAAAAATTTTAAAA
1 TTTTAAAAATTTTAAAA
1178946 GGCTTAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TTTTAAAAATTTTAAAA
Found at i:1186714 original size:22 final size:24
Alignment explanation
Indices: 1186638--1186850 Score: 133
Period size: 26 Copynumber: 8.2 Consensus size: 24
1186628 AAACGAAACA
** *
1186638 AAATAATATATGAAACAATTTGGAGT
1 AAATAATATA--AAACAATTTAAAAT
* * **
1186664 AAATAGTATAAAACAACTTAAAGC
1 AAATAATATAAAACAATTTAAAAT
*
1186688 AAATAATATGTAAAACAAATTAAAAT
1 AAATAATA--TAAAACAATTTAAAAT
1186714 AAATAATATACAAAGCAATTTAAAAT
1 AAATAATATA-AAA-CAATTTAAAAT
*
1186740 AAATAACATATAAGACAATTTAAAAT
1 AAAT-A-ATATAAAACAATTTAAAAT
*
1186766 AATATGTAAT-TAAAA-AGTTTAAAAT
1 AA-A--TAATATAAAACAATTTAAAAT
* *
1186791 AAATAATATGTAAAAAGAAGTTTCAAAT
1 AAATAATA--T-AAAACAA-TTTAAAAT
* *
1186819 AAATAATATACAAAACAGTTAAAAAT
1 AAATAATAT--AAAACAATTTAAAAT
1186845 AAATAA
1 AAATAA
1186851 ATGATGTGTA
Statistics
Matches: 151, Mismatches: 20, Indels: 32
0.74 0.10 0.16
Matches are distributed among these distances:
22 4 0.03
24 20 0.13
25 15 0.10
26 78 0.52
27 12 0.08
28 21 0.14
29 1 0.01
ACGTcount: A:0.60, C:0.06, G:0.07, T:0.27
Consensus pattern (24 bp):
AAATAATATAAAACAATTTAAAAT
Found at i:1186820 original size:28 final size:28
Alignment explanation
Indices: 1186762--1186827 Score: 98
Period size: 28 Copynumber: 2.3 Consensus size: 28
1186752 AGACAATTTA
1186762 AAATAATATGTAATTAAAAAGTTTAAAAT
1 AAATAATATGTAA-TAAAAAGTTTAAAAT
*
1186791 AAATAATATGTAA-AAAGAAGTTTCAAAT
1 AAATAATATGTAATAAA-AAGTTTAAAAT
1186819 AAATAATAT
1 AAATAATAT
1186828 ACAAAACAGT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
27 3 0.09
28 19 0.54
29 13 0.37
ACGTcount: A:0.59, C:0.02, G:0.08, T:0.32
Consensus pattern (28 bp):
AAATAATATGTAATAAAAAGTTTAAAAT
Found at i:1190302 original size:17 final size:17
Alignment explanation
Indices: 1190280--1190315 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
1190270 TTTTTTTTTT
1190280 TAATTTCCCATGAAGAA
1 TAATTTCCCATGAAGAA
1190297 TAATTTCCCATGAAGAA
1 TAATTTCCCATGAAGAA
1190314 TA
1 TA
1190316 TTAAGTGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.42, C:0.17, G:0.11, T:0.31
Consensus pattern (17 bp):
TAATTTCCCATGAAGAA
Found at i:1192829 original size:104 final size:105
Alignment explanation
Indices: 1192546--1192878 Score: 379
Period size: 97 Copynumber: 3.3 Consensus size: 105
1192536 ATCTTTAGAT
* * * * * *
1192546 TTTAGGG-TTTTAA-GAAAAAATTAAATAAATAAGGGTTTA-AAGTTTAGGGTTTCTTAATTAAA
1 TTTAGGGTTTTTAAGGAAAAAATCAAATAAATTAGGGTTTAGGA-TTTAAGGTTACTTAAGTAAA
* *
1192608 TTAATTATAAA--TTTTAAAAAATTAAATTAGAGTTTAGTA
65 TTAATTATAAATTTTTTAAAAAATTAGATTAGGGTTTAGTA
* * * * *
1192647 TTTATGGTTTTTAAGAAAAAAAGCAAATAAATTAGGGTTCAGG-----A--TTACTTTAGTAAAT
1 TTTAGGGTTTTTAAGGAAAAAATCAAATAAATTAGGGTTTAGGATTTAAGGTTACTTAAGTAAAT
* * * *
1192705 TAATTATAAA-TTTTAAAAAAAATAGATTAGGGTTTAATC
66 TAATTATAAATTTTTTAAAAAATTAGATTAGGGTTTAGTA
* *
1192744 TTTAGGGTTTTTAAGGAAAAAATTAAATAAATTAGGGTTTAGGATTTAAGGTTACTTGAGTAAAT
1 TTTAGGGTTTTTAAGGAAAAAATCAAATAAATTAGGGTTTAGGATTTAAGGTTACTTAAGTAAAT
*
1192809 TAATTATAAATTTTTTAAAAAATTAGATTGGGGTTTAGTA
66 TAATTATAAATTTTTTAAAAAATTAGATTAGGGTTTAGTA
1192849 TTTAGGGTTTTTAAGG-AAAAATCAAATAAA
1 TTTAGGGTTTTTAAGGAAAAAATCAAATAAA
1192879 GCTAATTTTA
Statistics
Matches: 191, Mismatches: 29, Indels: 21
0.79 0.12 0.09
Matches are distributed among these distances:
96 21 0.11
97 60 0.31
101 6 0.03
102 7 0.04
103 21 0.11
104 36 0.19
105 40 0.21
ACGTcount: A:0.43, C:0.02, G:0.16, T:0.39
Consensus pattern (105 bp):
TTTAGGGTTTTTAAGGAAAAAATCAAATAAATTAGGGTTTAGGATTTAAGGTTACTTAAGTAAAT
TAATTATAAATTTTTTAAAAAATTAGATTAGGGTTTAGTA
Found at i:1194221 original size:154 final size:152
Alignment explanation
Indices: 1193977--1194342 Score: 462
Period size: 154 Copynumber: 2.4 Consensus size: 152
1193967 TATAATGTAT
* * *
1193977 TAAAATAATAAAATTAGAAAATAGTATATTTTTTTAAAGTAATAAAATTCGGAAAAAAATATGAA
1 TAAAATAATAAAATTAGAAAATAATAAATTTTTTTAAAATAATAAAATTCGGAAAAAAATATGAA
* * * * *
1194042 TAAAGGGCTGAAATAAGGGCTTTTTTTAAATTTATTTAAAAAATACAGTAAATTAATATATTTCA
66 TAAAGGGCCGAAATAAGGGCTTTTTTAAAATTTATTTAAAAAATACACTAAATGAATACATTTCA
1194107 AACATAAAATACTAAAATAATG
131 AACATAAAATACTAAAATAATG
*
1194129 TAAAATAATAAAA-TACGAAAATAATAAATTTTTATTGAAAATAATAAAA-TCTGGGAAAAAATA
1 TAAAATAATAAAATTA-GAAAATAATAAATTTTT-TT-AAAATAATAAAATTC-GGAAAAAAATA
*
1194192 TGAATAAA-GGCCGAAATAAGGAGTTTTTTTAAAATTTATTTAAAAAATACACTAAATGAATACA
62 TGAATAAAGGGCCGAAATAAGG-GCTTTTTTAAAATTTATTTAAAAAATACACTAAATGAATACA
* **
1194256 TTTCAAATATAATGTACTAAAATAATG
126 TTTCAAACATAAAATACTAAAATAATG
* * * *
1194283 TAAAATTAGAAAATTAGAAAATAGT--A-TTTTTT-AAATAAATAAAA-TC-TAAAAAAATATGA
1 TAAAATAATAAAATTAGAAAATAATAAATTTTTTTAAAAT-AATAAAATTCGGAAAAAAATATGA
1194342 A
65 A
1194343 CAAAAGATCG
Statistics
Matches: 189, Mismatches: 18, Indels: 19
0.84 0.08 0.08
Matches are distributed among these distances:
147 12 0.06
148 4 0.02
149 9 0.05
150 2 0.01
151 6 0.03
152 29 0.15
153 16 0.08
154 109 0.58
155 2 0.01
ACGTcount: A:0.54, C:0.05, G:0.09, T:0.32
Consensus pattern (152 bp):
TAAAATAATAAAATTAGAAAATAATAAATTTTTTTAAAATAATAAAATTCGGAAAAAAATATGAA
TAAAGGGCCGAAATAAGGGCTTTTTTAAAATTTATTTAAAAAATACACTAAATGAATACATTTCA
AACATAAAATACTAAAATAATG
Found at i:1195448 original size:11 final size:12
Alignment explanation
Indices: 1195449--1195514 Score: 64
Period size: 11 Copynumber: 5.5 Consensus size: 12
1195439 TTTTAAAAAA
1195449 TAAAAAAGTATTT
1 TAAAAAA-TATTT
1195462 T-AAAAATATTT
1 TAAAAAATATTT
1195473 T-AAAAATATTT
1 TAAAAAATATTT
* ***
1195484 TAAAAATAAAAAA
1 TAAAAA-ATATTT
1195497 TAAAAAATATTT
1 TAAAAAATATTT
1195509 TAAAAA
1 TAAAAA
1195515 TAAATATATT
Statistics
Matches: 43, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
11 17 0.40
12 17 0.40
13 9 0.21
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.35
Consensus pattern (12 bp):
TAAAAAATATTT
Found at i:1195495 original size:17 final size:18
Alignment explanation
Indices: 1195432--1195498 Score: 73
Period size: 18 Copynumber: 3.4 Consensus size: 18
1195422 AATAAACACC
1195432 AAAAAAT-TTTTAAAAAAT
1 AAAAAATATTTT-AAAAAT
1195450 AAAAAAGTATTTTAAAAAT
1 AAAAAA-TATTTTAAAAAT
1195469 ATTTTAAAAATATTTTAAAAAT
1 A----AAAAATATTTTAAAAAT
1195491 AAAAAATA
1 AAAAAATA
1195499 AAAAATATTT
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
18 13 0.30
19 8 0.19
20 4 0.09
22 13 0.30
23 5 0.12
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.34
Consensus pattern (18 bp):
AAAAAATATTTTAAAAAT
Found at i:1204452 original size:28 final size:28
Alignment explanation
Indices: 1204421--1204482 Score: 124
Period size: 28 Copynumber: 2.2 Consensus size: 28
1204411 CAAATTACTA
1204421 TAGCAACCAAGGCATTAATAAAGAACTC
1 TAGCAACCAAGGCATTAATAAAGAACTC
1204449 TAGCAACCAAGGCATTAATAAAGAACTC
1 TAGCAACCAAGGCATTAATAAAGAACTC
1204477 TAGCAA
1 TAGCAA
1204483 AAGCAAAGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.47, C:0.21, G:0.15, T:0.18
Consensus pattern (28 bp):
TAGCAACCAAGGCATTAATAAAGAACTC
Found at i:1210455 original size:22 final size:20
Alignment explanation
Indices: 1210407--1210449 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
1210397 AAATGTAGTG
* *
1210407 TATTTTTAAAATAAAAAATA
1 TATTTTAAAAATAAAAAAAA
1210427 TATTTTAAAAATAAAAAAAA
1 TATTTTAAAAATAAAAAAAA
1210447 TAT
1 TAT
1210450 GATTTATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
TATTTTAAAAATAAAAAAAA
Found at i:1227878 original size:31 final size:31
Alignment explanation
Indices: 1227829--1227891 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
1227819 GTCACAAAAT
*
1227829 AGTCACCGAGCTACTTGAACA-TTTTCATTTA
1 AGTCACCGAACTACTTGAA-AGTTTTCATTTA
* * *
1227860 AGTCATCGAACTATTTGAAAGTTTTTATTTA
1 AGTCACCGAACTACTTGAAAGTTTTCATTTA
1227891 A
1 A
1227892 ATTATTGGGT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 1 0.04
31 26 0.96
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.40
Consensus pattern (31 bp):
AGTCACCGAACTACTTGAAAGTTTTCATTTA
Found at i:1231046 original size:2 final size:2
Alignment explanation
Indices: 1231039--1231070 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1231029 ATGGTGAATA
1231039 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1231071 TAAAGNNNNN
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1231187 original size:2 final size:2
Alignment explanation
Indices: 1231180--1231211 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1231170 NNNNNNAGTA
1231180 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1231212 TAAAGAAGGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1240668 original size:24 final size:24
Alignment explanation
Indices: 1240635--1240685 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1240625 TACACAAATA
* * *
1240635 TGAGACAAAAGTCTTGTTTTATTT
1 TGAGACAAAACTATTGTTGTATTT
*
1240659 TGAGAGAAAACTATTGTTGTATTT
1 TGAGACAAAACTATTGTTGTATTT
1240683 TGA
1 TGA
1240686 TAAAAATAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.31, C:0.06, G:0.20, T:0.43
Consensus pattern (24 bp):
TGAGACAAAACTATTGTTGTATTT
Found at i:1244045 original size:11 final size:11
Alignment explanation
Indices: 1244031--1244079 Score: 89
Period size: 11 Copynumber: 4.5 Consensus size: 11
1244021 TATTTTTTAA
1244031 TTTTAAAATAC
1 TTTTAAAATAC
1244042 TTTTAAAATAC
1 TTTTAAAATAC
1244053 TTTTAAAATAC
1 TTTTAAAATAC
*
1244064 TTTTAAAATAT
1 TTTTAAAATAC
1244075 TTTTA
1 TTTTA
1244080 TTTTTAAAAC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
11 37 1.00
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:1247847 original size:26 final size:26
Alignment explanation
Indices: 1247821--1247869 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
1247811 ATAAATTAAT
1247821 TTAAATGAAAT-TTAATATTATGAAA
1 TTAAATGAAATGTTAATATTATGAAA
* * *
1247846 TTAATTTAAGTGTTAATATTATGA
1 TTAAATGAAATGTTAATATTATGA
1247870 TATATATATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 8 0.40
26 12 0.60
ACGTcount: A:0.45, C:0.00, G:0.10, T:0.45
Consensus pattern (26 bp):
TTAAATGAAATGTTAATATTATGAAA
Found at i:1250719 original size:2 final size:2
Alignment explanation
Indices: 1250712--1250743 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1250702 TTCCTCCCAA
1250712 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1250744 TTAAGCACAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.