Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D07
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: 56457815
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1765025 characters in sequence are not A, C, G, or T
File 106 of 189
Found at i:29603379 original size:15 final size:16
Alignment explanation
Indices: 29603344--29603379 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
29603334 AGGTGTGTAG
29603344 GAATGATATTTGCATT
1 GAATGATATTTGCATT
29603360 GAATGATATTTGCA-T
1 GAATGATATTTGCATT
29603375 GAATG
1 GAATG
29603380 CAGAATGTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.33, C:0.06, G:0.22, T:0.39
Consensus pattern (16 bp):
GAATGATATTTGCATT
Found at i:29604182 original size:97 final size:98
Alignment explanation
Indices: 29604047--29604252 Score: 265
Period size: 97 Copynumber: 2.1 Consensus size: 98
29604037 GAAAAATGCT
* * *
29604047 TGAAAAAGATTATCAAAATGGACAAGATGAAATTTTATTGAGAACA-AGGCTTAAAATGACTAAA
1 TGAATAAGATTATCAAAATGGACAAGATGAAATTTTATTGAGAACACA-GCTCAAAATGAATAAA
*
29604111 TTAATCAAAATAGAAAATTTTGCTAAGATA-AGA
65 TTAATCAAAATAGAAAATTTTGCTAAGATACAAA
* * * *
29604144 TGAATAAGATTATCACAGTGGATAAGATGGAAA-TTTATTGAGAGCACAGCTCAAAATGAATAAA
1 TGAATAAGATTATCAAAATGGACAAGAT-GAAATTTTATTGAGAACACAGCTCAAAATGAATAAA
* * *
29604208 TTAATCGAGATAGCAAATTTTGCTAAGATACGAAA
65 TTAATCAAAATAGAAAATTTTGCTAAGATAC-AAA
29604243 TGAATAAGAT
1 TGAATAAGAT
29604253 GAAAACAGGT
Statistics
Matches: 94, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
97 77 0.82
98 5 0.05
99 12 0.13
ACGTcount: A:0.48, C:0.08, G:0.17, T:0.27
Consensus pattern (98 bp):
TGAATAAGATTATCAAAATGGACAAGATGAAATTTTATTGAGAACACAGCTCAAAATGAATAAAT
TAATCAAAATAGAAAATTTTGCTAAGATACAAA
Found at i:29604538 original size:5 final size:5
Alignment explanation
Indices: 29604522--29604586 Score: 55
Period size: 5 Copynumber: 12.8 Consensus size: 5
29604512 GGCCTCTCTT
*
29604522 TTTTC ATTTTC TTTTC TTTT- TTCTTT TTTTC TTTTC -TTTC TTTTTC
1 TTTTC -TTTTC TTTTC TTTTC TT-TTC TTTTC TTTTC TTTTC -TTTTC
*
29604568 TTTTTC TTATC TTTT- TTTT
1 -TTTTC TTTTC TTTTC TTTT
29604587 TTGAAAATTC
Statistics
Matches: 52, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
4 10 0.19
5 25 0.48
6 17 0.33
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTC
Found at i:29604543 original size:20 final size:20
Alignment explanation
Indices: 29604520--29604586 Score: 91
Period size: 20 Copynumber: 3.3 Consensus size: 20
29604510 TTGGCCTCTC
*
29604520 TTTTTTCATTTTCTTTTCTT
1 TTTTTTCTTTTTCTTTTCTT
29604540 TTTTCTT-TTTTTCTTTTCTT
1 TTTT-TTCTTTTTCTTTTCTT
*
29604560 TCTTTTTCTTTTTCTTATCTT
1 T-TTTTTCTTTTTCTTTTCTT
29604581 TTTTTT
1 TTTTTT
29604587 TTGAAAATTC
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
20 24 0.57
21 18 0.43
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (20 bp):
TTTTTTCTTTTTCTTTTCTT
Found at i:29604547 original size:25 final size:24
Alignment explanation
Indices: 29604518--29604588 Score: 87
Period size: 21 Copynumber: 3.0 Consensus size: 24
29604508 CCTTGGCCTC
29604518 TCTTTTTTCATTTTCTTTTCTTTTT
1 TCTTTTTTC-TTTTCTTTTCTTTTT
29604543 TCTTTTTTTCTTTTC-TTTC-TTTT
1 TC-TTTTTTCTTTTCTTTTCTTTTT
*
29604566 TC-TTTTTCTTATCTTTT-TTTTT
1 TCTTTTTTCTTTTCTTTTCTTTTT
29604588 T
1 T
29604589 GAAAATTCTT
Statistics
Matches: 42, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
21 10 0.24
22 8 0.19
23 6 0.14
24 4 0.10
25 7 0.17
26 7 0.17
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (24 bp):
TCTTTTTTCTTTTCTTTTCTTTTT
Found at i:29604585 original size:29 final size:30
Alignment explanation
Indices: 29604520--29604585 Score: 75
Period size: 29 Copynumber: 2.2 Consensus size: 30
29604510 TTGGCCTCTC
*
29604520 TTTTTTCATTTTCTTTTCTTTTTTCTTTTT
1 TTTTTTCATTTTCTTTTCTTTTTTCTTTCT
29604550 TTCTTTTC--TTTCTTTT-TCTTTTTCTTATCT
1 TT-TTTTCATTTTCTTTTCT-TTTTTCTT-TCT
29604580 TTTTTT
1 TTTTTT
29604586 TTTGAAAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
28 1 0.03
29 20 0.62
30 6 0.19
31 5 0.16
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (30 bp):
TTTTTTCATTTTCTTTTCTTTTTTCTTTCT
Found at i:29606827 original size:19 final size:19
Alignment explanation
Indices: 29606803--29606845 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
29606793 GTGAAAATCT
* *
29606803 AATGCATATG-ATGCAATG
1 AATGCACATGCATGAAATG
29606821 CAATGCACATGCATGAAATG
1 -AATGCACATGCATGAAATG
29606841 AATGC
1 AATGC
29606846 CTAAAGAGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.40, C:0.16, G:0.21, T:0.23
Consensus pattern (19 bp):
AATGCACATGCATGAAATG
Found at i:29609201 original size:3 final size:3
Alignment explanation
Indices: 29609193--29609217 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
29609183 AGATAAGTAG
29609193 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
29609218 AATTGCCAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:29610171 original size:17 final size:16
Alignment explanation
Indices: 29610146--29610182 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
29610136 AACCTACTGC
*
29610146 CTTTTCTTTGTTTCTTT
1 CTTTCCTTTGTTTC-TT
29610163 CTTTCCTTTGTTTCTT
1 CTTTCCTTTGTTTCTT
29610179 CTTT
1 CTTT
29610183 GCAGGTGACG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.00, C:0.22, G:0.05, T:0.73
Consensus pattern (16 bp):
CTTTCCTTTGTTTCTT
Found at i:29612221 original size:8 final size:8
Alignment explanation
Indices: 29612202--29612242 Score: 59
Period size: 8 Copynumber: 5.4 Consensus size: 8
29612192 ACTTTACTTT
29612202 ATATAA-A
1 ATATAATA
29612209 ATATAATA
1 ATATAATA
29612217 ATATAATA
1 ATATAATA
29612225 ATATAAT-
1 ATATAATA
*
29612232 ATATAAAA
1 ATATAATA
29612240 ATA
1 ATA
29612243 AAACTTAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
7 12 0.39
8 19 0.61
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (8 bp):
ATATAATA
Found at i:29612243 original size:13 final size:14
Alignment explanation
Indices: 29612201--29612243 Score: 61
Period size: 15 Copynumber: 3.0 Consensus size: 14
29612191 TACTTTACTT
29612201 TATATAAAATATAA
1 TATATAAAATATAA
29612215 TAATATAATAATATAA
1 T-ATATAA-AATATAA
29612231 TATATAAAA-ATAA
1 TATATAAAATATAA
29612244 AACTTAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
13 4 0.15
14 3 0.11
15 12 0.44
16 8 0.30
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
TATATAAAATATAA
Found at i:29613974 original size:31 final size:31
Alignment explanation
Indices: 29613935--29614004 Score: 115
Period size: 31 Copynumber: 2.3 Consensus size: 31
29613925 TCCTCAAATG
*
29613935 CAAG-CAATGTGAACCATTATAGTTTACATA
1 CAAGACAATGTGAACCATTATAGTATACATA
*
29613965 CAAGACAATGTGAACCATTATAGTATACATG
1 CAAGACAATGTGAACCATTATAGTATACATA
29613996 CAAGACAAT
1 CAAGACAAT
29614005 CTCCTTAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
30 4 0.11
31 33 0.89
ACGTcount: A:0.43, C:0.17, G:0.14, T:0.26
Consensus pattern (31 bp):
CAAGACAATGTGAACCATTATAGTATACATA
Found at i:29623491 original size:16 final size:15
Alignment explanation
Indices: 29623472--29623504 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
29623462 GTTTACATGT
*
29623472 AAAAGGTTTTACGGA
1 AAAAAGTTTTACGGA
29623487 AAAAAGTTTTACGGA
1 AAAAAGTTTTACGGA
29623502 AAA
1 AAA
29623505 TGCTTTCTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.48, C:0.06, G:0.21, T:0.24
Consensus pattern (15 bp):
AAAAAGTTTTACGGA
Found at i:29623826 original size:16 final size:17
Alignment explanation
Indices: 29623805--29623863 Score: 66
Period size: 16 Copynumber: 3.2 Consensus size: 17
29623795 ATATTTAGTC
29623805 ATATAATAAATTA-TTA
1 ATATAATAAATTATTTA
29623821 ATATAATAAATATAATTTA
1 ATATAATAAAT-T-ATTTA
29623840 TTATATTAATAAATTATTTA
1 --ATA-TAATAAATTATTTA
29623860 ATAT
1 ATAT
29623864 TTTAATTTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
16 11 0.30
17 2 0.05
18 4 0.11
19 3 0.08
20 5 0.14
21 4 0.11
22 8 0.22
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATATAATAAATTATTTA
Found at i:29623835 original size:22 final size:22
Alignment explanation
Indices: 29623810--29623853 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
29623800 TAGTCATATA
29623810 ATAAATTATTA-ATATAATAAAT
1 ATAAATTATTATAT-TAATAAAT
*
29623832 ATAATTTATTATATTAATAAAT
1 ATAAATTATTATATTAATAAAT
29623854 TATTTAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 18 0.90
23 2 0.10
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
ATAAATTATTATATTAATAAAT
Found at i:29626711 original size:22 final size:22
Alignment explanation
Indices: 29626686--29626741 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
29626676 AACTGTTTGG
**
29626686 TGACATCACGATGTAGAAGAGA
1 TGACATCACGACATAGAAGAGA
*
29626708 TGACATTACGACATAGAAGAGA
1 TGACATCACGACATAGAAGAGA
*
29626730 TGACACCACGAC
1 TGACATCACGAC
29626742 TTTAGACTTG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.41, C:0.20, G:0.23, T:0.16
Consensus pattern (22 bp):
TGACATCACGACATAGAAGAGA
Found at i:29627080 original size:12 final size:12
Alignment explanation
Indices: 29627065--29627089 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29627055 TTAATTCTCA
29627065 AGTCATTTCTAT
1 AGTCATTTCTAT
29627077 AGTCATTTCTAT
1 AGTCATTTCTAT
29627089 A
1 A
29627090 CTCAGTGAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.16, G:0.08, T:0.48
Consensus pattern (12 bp):
AGTCATTTCTAT
Found at i:29630593 original size:9 final size:9
Alignment explanation
Indices: 29630567--29630594 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
29630557 AGAAAACTGA
29630567 AAAGAAAAT
1 AAAGAAAAT
29630576 AAAGAAAAT
1 AAAGAAAAT
29630585 AAAGAAAAT
1 AAAGAAAAT
29630594 A
1 A
29630595 GATCAGTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.79, C:0.00, G:0.11, T:0.11
Consensus pattern (9 bp):
AAAGAAAAT
Found at i:29632083 original size:3 final size:3
Alignment explanation
Indices: 29632051--29632123 Score: 53
Period size: 3 Copynumber: 24.3 Consensus size: 3
29632041 AATAAGACTC
* * * * *
29632051 ATA ATC ATA AAA ATA ATA AGA CTA AGTA ATA ATA AT- ATA AGA A-A
1 ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA
29632095 ATA ATAA ATGA A-A ATA ATA ATA ATA ATA A
1 ATA AT-A AT-A ATA ATA ATA ATA ATA ATA A
29632124 CTAAAAAAAT
Statistics
Matches: 55, Mismatches: 10, Indels: 10
0.73 0.13 0.13
Matches are distributed among these distances:
2 6 0.11
3 41 0.75
4 8 0.15
ACGTcount: A:0.66, C:0.03, G:0.05, T:0.26
Consensus pattern (3 bp):
ATA
Found at i:29632097 original size:13 final size:13
Alignment explanation
Indices: 29632081--29632114 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
29632071 ACTAAGTAAT
29632081 AATAATATAA-GAA
1 AATAATA-AATGAA
29632094 AATAATAAATGAA
1 AATAATAAATGAA
29632107 AATAATAA
1 AATAATAA
29632115 TAATAATAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 2 0.10
13 18 0.90
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.24
Consensus pattern (13 bp):
AATAATAAATGAA
Found at i:29632097 original size:16 final size:16
Alignment explanation
Indices: 29632060--29632116 Score: 59
Period size: 16 Copynumber: 3.8 Consensus size: 16
29632050 CATAATCATA
*
29632060 AAAATAATAAGACTAAG
1 AAAATAATAATA-TAAG
*
29632077 -TAATAATAATATAAG
1 AAAATAATAATATAAG
29632092 AAAATAATAA-AT--G
1 AAAATAATAATATAAG
29632105 AAAATAATAATA
1 AAAATAATAATA
29632117 ATAATAACTA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
13 11 0.31
14 1 0.03
15 6 0.17
16 17 0.49
ACGTcount: A:0.67, C:0.02, G:0.07, T:0.25
Consensus pattern (16 bp):
AAAATAATAATATAAG
Found at i:29632245 original size:3 final size:3
Alignment explanation
Indices: 29632229--29632297 Score: 54
Period size: 3 Copynumber: 22.7 Consensus size: 3
29632219 GAAATATAGG
*
29632229 AAT AAT AA- ATAT AAT AAT AA- ATAT AAT AAC AAT AAAT AAT AAT GAA-
1 AAT AAT AAT A-AT AAT AAT AAT A-AT AAT AAT AAT -AAT AAT AAT -AAT
* *
29632275 AAT ACT AAT AAT AAG AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AA
29632298 ATAAAAAGAA
Statistics
Matches: 53, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
2 4 0.08
3 42 0.79
4 7 0.13
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:29632246 original size:12 final size:12
Alignment explanation
Indices: 29632229--29632302 Score: 69
Period size: 12 Copynumber: 5.8 Consensus size: 12
29632219 GAAATATAGG
29632229 AATAATAAATAT
1 AATAATAAATAT
29632241 AATAATAAATAT
1 AATAATAAATAT
* *
29632253 AATAACAATAAAT
1 AATAATAA-ATAT
29632266 AATAATGAAAATACT
1 AATAAT--AAATA-T
29632281 AATAATAAGA-AT
1 AATAATAA-ATAT
29632293 AATAAATAAA
1 AAT-AATAAA
29632303 AAGAAACAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
12 24 0.46
13 16 0.31
14 3 0.06
15 9 0.17
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.27
Consensus pattern (12 bp):
AATAATAAATAT
Found at i:29632257 original size:15 final size:16
Alignment explanation
Indices: 29632239--29632301 Score: 67
Period size: 16 Copynumber: 3.9 Consensus size: 16
29632229 AATAATAAAT
29632239 ATAATAATAAAT-ATA
1 ATAATAATAAATAATA
*
29632254 ATAACAATAAATAATA
1 ATAATAATAAATAATA
29632270 ATGAA-AATACTAATAATA
1 AT-AATAATA--AATAATA
*
29632288 AGAATAATAAATAA
1 ATAATAATAAATAA
29632302 AAAGAAACAA
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
15 11 0.27
16 14 0.34
17 4 0.10
18 12 0.29
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.27
Consensus pattern (16 bp):
ATAATAATAAATAATA
Found at i:29635994 original size:11 final size:11
Alignment explanation
Indices: 29635944--29635996 Score: 54
Period size: 11 Copynumber: 4.6 Consensus size: 11
29635934 ATAAAAGCTC
29635944 TAAAATA-AAT
1 TAAAATAGAAT
29635954 TAAATATATGAAT
1 TAAA-ATA-GAAT
*
29635967 TCAAAATAGACT
1 T-AAAATAGAAT
*
29635979 CAAAATAGAAT
1 TAAAATAGAAT
29635990 TAAAATA
1 TAAAATA
29635997 ACCATTGAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
10 4 0.11
11 18 0.51
12 3 0.09
13 7 0.20
14 3 0.09
ACGTcount: A:0.60, C:0.06, G:0.06, T:0.28
Consensus pattern (11 bp):
TAAAATAGAAT
Found at i:29638804 original size:16 final size:16
Alignment explanation
Indices: 29638783--29638815 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
29638773 TTAATCTACA
29638783 GTTTTTATTAT-TATAT
1 GTTTTT-TTATCTATAT
29638799 GTTTTTTTATCTATAT
1 GTTTTTTTATCTATAT
29638815 G
1 G
29638816 CTAAGAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.21, C:0.03, G:0.09, T:0.67
Consensus pattern (16 bp):
GTTTTTTTATCTATAT
Found at i:29655442 original size:20 final size:20
Alignment explanation
Indices: 29655405--29655442 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
29655395 TCTGAAATTG
**
29655405 TTTTATTTATAAGTTTATCA
1 TTTTATTTATAAAATTATCA
29655425 TTTTATTTATAAAATTAT
1 TTTTATTTATAAAATTAT
29655443 TACTTTAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.61
Consensus pattern (20 bp):
TTTTATTTATAAAATTATCA
Found at i:29655449 original size:20 final size:20
Alignment explanation
Indices: 29655406--29655449 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
29655396 CTGAAATTGT
** *
29655406 TTTATTTATAAGTTTATCAT
1 TTTATTTATAAAATTATCAC
*
29655426 TTTATTTATAAAATTATTAC
1 TTTATTTATAAAATTATCAC
29655446 TTTA
1 TTTA
29655450 ATAAATAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59
Consensus pattern (20 bp):
TTTATTTATAAAATTATCAC
Found at i:29658599 original size:20 final size:20
Alignment explanation
Indices: 29658558--29658601 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
29658548 TTAAATTGTT
* *
29658558 TTTTGAATTATTAGTCTTAA
1 TTTTGAATTAGTACTCTTAA
29658578 TTTTGAATTAGTACT-TTGAA
1 TTTTGAATTAGTACTCTT-AA
29658598 TTTT
1 TTTT
29658602 TATATAACTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.27, C:0.05, G:0.11, T:0.57
Consensus pattern (20 bp):
TTTTGAATTAGTACTCTTAA
Found at i:29662669 original size:44 final size:45
Alignment explanation
Indices: 29662602--29662686 Score: 138
Period size: 44 Copynumber: 1.9 Consensus size: 45
29662592 TGAACATTAA
*
29662602 ATTTTATTTTTAATGATTTTTAAAGTGCTT-ATAACATTCTATAAT
1 ATTTTATTTATAATGATTTTTAAAGTG-TTCATAACATTCTATAAT
29662647 ATTTTATTTAT-ATGATTTTTAAAGTGTTCATAACATTCTA
1 ATTTTATTTATAATGATTTTTAAAGTGTTCATAACATTCTA
29662687 ATTCATAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
43 2 0.05
44 26 0.68
45 10 0.26
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.53
Consensus pattern (45 bp):
ATTTTATTTATAATGATTTTTAAAGTGTTCATAACATTCTATAAT
Found at i:29670144 original size:12 final size:12
Alignment explanation
Indices: 29670127--29670151 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29670117 ATTAAATCCC
29670127 TGTACTTTCCTA
1 TGTACTTTCCTA
29670139 TGTACTTTCCTA
1 TGTACTTTCCTA
29670151 T
1 T
29670152 CTCTCCCTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.08, T:0.52
Consensus pattern (12 bp):
TGTACTTTCCTA
Found at i:29675917 original size:48 final size:48
Alignment explanation
Indices: 29675844--29676013 Score: 232
Period size: 48 Copynumber: 3.5 Consensus size: 48
29675834 GGTCGCATAT
* * *
29675844 GTGGCACGGACTGTGTGTAGACCACCAATATTCTGTTAAGATACAAGG
1 GTGGCACGGACTGTGTGCAGGCCACCAATATTCTGTTAAGATACAAAG
29675892 GTGGCACGGACTGTGTGCAGGCCACCAATATTCTGTTAAGATACAAAG
1 GTGGCACGGACTGTGTGCAGGCCACCAATATTCTGTTAAGATACAAAG
* * * ** *
29675940 GTGGCACGGACTGTGTGCAGGCCACCGAGAGTCTGTTATTACACAAAG
1 GTGGCACGGACTGTGTGCAGGCCACCAATATTCTGTTAAGATACAAAG
* * *
29675988 GTGGTAAGGACTGTGTGTAGGCCACC
1 GTGGCACGGACTGTGTGCAGGCCACC
29676014 GAGAAATCTG
Statistics
Matches: 110, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 110 1.00
ACGTcount: A:0.26, C:0.21, G:0.30, T:0.23
Consensus pattern (48 bp):
GTGGCACGGACTGTGTGCAGGCCACCAATATTCTGTTAAGATACAAAG
Found at i:29678329 original size:21 final size:21
Alignment explanation
Indices: 29678303--29678354 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
29678293 AAAACCCAAC
*
29678303 GAGTATCGATACTTTTTAAAT
1 GAGTATCAATACTTTTTAAAT
*
29678324 GAGTATCAATATTTTTTAAA-
1 GAGTATCAATACTTTTTAAAT
*
29678344 AAGTATCAATA
1 GAGTATCAATA
29678355 AAATAGTACC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 10 0.36
21 18 0.64
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (21 bp):
GAGTATCAATACTTTTTAAAT
Found at i:29680410 original size:21 final size:19
Alignment explanation
Indices: 29680336--29680415 Score: 52
Period size: 21 Copynumber: 3.9 Consensus size: 19
29680326 TGTGTGCCTC
*
29680336 GGCCGTGTGAAGAACAACAT
1 GGCCATGTGAAGAAC-ACAT
* * * *
29680356 GGTCGTGTAGAGGAACACAC
1 GGCCATGT-GAAGAACACAT
*
29680376 GCCCATGTGTAAGAAGCACAT
1 GGCCATGTG-AAGAA-CACAT
29680397 GGCCATGTAGAAGAGACAC
1 GGCCATGT-GAAGA-ACAC
29680416 GCGCTCGTGT
Statistics
Matches: 46, Mismatches: 9, Indels: 9
0.72 0.14 0.14
Matches are distributed among these distances:
19 1 0.02
20 19 0.41
21 24 0.52
22 2 0.04
ACGTcount: A:0.34, C:0.21, G:0.30, T:0.15
Consensus pattern (19 bp):
GGCCATGTGAAGAACACAT
Found at i:29690504 original size:15 final size:15
Alignment explanation
Indices: 29690480--29690511 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
29690470 TATGCATGCA
*
29690480 AAATATAAAAGACAT
1 AAATACAAAAGACAT
29690495 AAATACAAAAGACAT
1 AAATACAAAAGACAT
29690510 AA
1 AA
29690512 CAGTGAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.69, C:0.09, G:0.06, T:0.16
Consensus pattern (15 bp):
AAATACAAAAGACAT
Found at i:29692699 original size:15 final size:16
Alignment explanation
Indices: 29692677--29692715 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
29692667 TGTTTGGTTC
29692677 GCTGTAAT-GAATAAA
1 GCTGTAATGGAATAAA
* *
29692692 GGTGTAATGGAATAGA
1 GCTGTAATGGAATAAA
29692708 GCTGTAAT
1 GCTGTAAT
29692716 AGTAATTTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.38, C:0.05, G:0.28, T:0.28
Consensus pattern (16 bp):
GCTGTAATGGAATAAA
Found at i:29692761 original size:45 final size:44
Alignment explanation
Indices: 29692697--29692789 Score: 143
Period size: 45 Copynumber: 2.1 Consensus size: 44
29692687 ATAAAGGTGT
*
29692697 AATGGAATAGAGCTGTAATAGTAATTTAAT-TGTTTGGTTGAATGG
1 AATGGAATAGAACTGTAATAGT-A-TTAATGTGTTTGGTTGAATGG
*
29692742 AATGGAATAGAACTGTAATAGTATTATTGTGTTTGGTTGAATGG
1 AATGGAATAGAACTGTAATAGTATTAATGTGTTTGGTTGAATGG
29692786 AATG
1 AATG
29692790 ATGTTGTAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
43 4 0.09
44 20 0.44
45 21 0.47
ACGTcount: A:0.33, C:0.02, G:0.27, T:0.38
Consensus pattern (44 bp):
AATGGAATAGAACTGTAATAGTATTAATGTGTTTGGTTGAATGG
Found at i:29692798 original size:39 final size:41
Alignment explanation
Indices: 29692697--29692801 Score: 110
Period size: 44 Copynumber: 2.5 Consensus size: 41
29692687 ATAAAGGTGT
29692697 AATGGAATAGA-GCTGTAATAGTAATTTAATTGTTTGGTTG
1 AATGGAATAGATGCTGTAATAGTAATTTAATTGTTTGGTTG
* *
29692737 AATGGAATGGAATAGAACTGTAATAGT-A-TTATTGTGTTTGGTTG
1 AATGGAATAG-AT-G--CTGTAATAGTAATTTAAT-TGTTTGGTTG
*
29692781 AATGGAAT-GATGTTGTAATAG
1 AATGGAATAGATGCTGTAATAG
29692802 CATAAGGAAA
Statistics
Matches: 56, Mismatches: 3, Indels: 13
0.78 0.04 0.18
Matches are distributed among these distances:
39 8 0.14
40 9 0.16
41 2 0.04
42 2 0.04
43 6 0.11
44 19 0.34
45 10 0.18
ACGTcount: A:0.33, C:0.02, G:0.27, T:0.38
Consensus pattern (41 bp):
AATGGAATAGATGCTGTAATAGTAATTTAATTGTTTGGTTG
Found at i:29692977 original size:56 final size:57
Alignment explanation
Indices: 29692896--29693024 Score: 147
Period size: 56 Copynumber: 2.3 Consensus size: 57
29692886 AATAAGATTA
* * *
29692896 TTAATATAAATAATAAATATTTTAATCATATT-TTAACATAATTATTATTAAATAT-AAT
1 TTAATA-AAATAATAAATAATTTAATAAAATTCTTAACATAATTATTATT--ATATGAAT
* * *
29692954 TTAATAAAA-AATATATAATTTAATAAAATTCTTAATATAATTATTCTTATATGAAT
1 TTAATAAAATAATAAATAATTTAATAAAATTCTTAACATAATTATTATTATATGAAT
*
29693010 TTAATAAAATCATAA
1 TTAATAAAATAATAA
29693025 TATATAATAA
Statistics
Matches: 60, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
55 4 0.07
56 29 0.48
57 21 0.35
58 6 0.10
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (57 bp):
TTAATAAAATAATAAATAATTTAATAAAATTCTTAACATAATTATTATTATATGAAT
Found at i:29695959 original size:475 final size:475
Alignment explanation
Indices: 29695069--29695997 Score: 1849
Period size: 475 Copynumber: 2.0 Consensus size: 475
29695059 ATATCATCGG
29695069 CTGATGTTAGCTTATTTGATGAAACATCTAATACTTGGAGGTTGACCAATTTTGATAGGTCTTCC
1 CTGATGTTAGCTTATTTGATGAAACATCTAATACTTGGAGGTTGACCAATTTTGATAGGTCTTCC
29695134 ATTTTTGCAATACCATTGTGGCTCAAGTATATTTCTTCTAAGGCATTGCATTCCTTGAAAACAAA
66 ATTTTTGCAATACCATTGTGGCTCAAGTATATTTCTTCTAAGGCATTGCATTCCTTGAAAACAAA
29695199 AAATCTAGAGAAAAACCTCATCCAAATATTACGACATTAAAATTTTTATGAGAACCAACATTTTT
131 AAATCTAGAGAAAAACCTCATCCAAATATTACGACATTAAAATTTTTATGAGAACCAACATTTTT
*
29695264 TAAGGTGCTATACCTCCAACCCTATCATAGATGTTAACTGGTTACTTTGCAAGCTAATCTTCTTG
196 TAAAGTGCTATACCTCCAACCCTATCATAGATGTTAACTGGTTACTTTGCAAGCTAATCTTCTTG
29695329 ATGCAGCTCATAAAGGTTAATCACTTTAATTCAGTTTCTTCCTAGCCACAGTTCTTGTAACTTTG
261 ATGCAGCTCATAAAGGTTAATCACTTTAATTCAGTTTCTTCCTAGCCACAGTTCTTGTAACTTTG
29695394 TAAAATTTTGCAAATTTTCCATCACCTAAGATACCAAGATCAGTGAAAGCAATTCACAAATTAGA
326 TAAAATTTTGCAAATTTTCCATCACCTAAGATACCAAGATCAGTGAAAGCAATTCACAAATTAGA
29695459 CCATGCTCAAGAAATTACTAATAACTGACCAATCTTACCCCCTACTTCAATACTGAAACAAAAAT
391 CCATGCTCAAGAAATTACTAATAACTGACCAATCTTACCCCCTACTTCAATACTGAAACAAAAAT
29695524 TGACAAAAAGCTTGATAGGT
456 TGACAAAAAGCTTGATAGGT
29695544 CTGATGTTAGCTTATTTGATGAAACATCTAATACTTGGAGGTTGACCAATTTTGATAGGTCTTCC
1 CTGATGTTAGCTTATTTGATGAAACATCTAATACTTGGAGGTTGACCAATTTTGATAGGTCTTCC
29695609 ATTTTTGCAATACCATTGTGGCTCAAGTATATTTCTTCTAAGGCATTGCATTCCTTGAAAACAAA
66 ATTTTTGCAATACCATTGTGGCTCAAGTATATTTCTTCTAAGGCATTGCATTCCTTGAAAACAAA
29695674 AAATCTAGAGAAAAACCTCATCCAAATATTACGACATTAAAATTTTTATGAGAACCAACATTTTT
131 AAATCTAGAGAAAAACCTCATCCAAATATTACGACATTAAAATTTTTATGAGAACCAACATTTTT
29695739 TAAAGTGCTATACCTCCAACCCTATCATAGATGTTAACTGGTTACTTTGCAAGCTAATCTTCTTG
196 TAAAGTGCTATACCTCCAACCCTATCATAGATGTTAACTGGTTACTTTGCAAGCTAATCTTCTTG
29695804 ATGCAGCTCATAAAGGTTAATCACTTTAATTCAGTTTCTTCCTAGCCACAGTTCTTGTAACTTTG
261 ATGCAGCTCATAAAGGTTAATCACTTTAATTCAGTTTCTTCCTAGCCACAGTTCTTGTAACTTTG
29695869 TAAAATTTTGCAAATTTTCCATCACCTAAGATACCAAGATCAGTGAAAGCAATTCACAAATTAGA
326 TAAAATTTTGCAAATTTTCCATCACCTAAGATACCAAGATCAGTGAAAGCAATTCACAAATTAGA
29695934 CCATGCTCAAGAAATTACTAATAACTGACCAATCTTACCCCCTACTTCAATACTGAAACAAAAA
391 CCATGCTCAAGAAATTACTAATAACTGACCAATCTTACCCCCTACTTCAATACTGAAACAAAAA
29695998 GCTTATGCCA
Statistics
Matches: 453, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
475 453 1.00
ACGTcount: A:0.34, C:0.20, G:0.13, T:0.33
Consensus pattern (475 bp):
CTGATGTTAGCTTATTTGATGAAACATCTAATACTTGGAGGTTGACCAATTTTGATAGGTCTTCC
ATTTTTGCAATACCATTGTGGCTCAAGTATATTTCTTCTAAGGCATTGCATTCCTTGAAAACAAA
AAATCTAGAGAAAAACCTCATCCAAATATTACGACATTAAAATTTTTATGAGAACCAACATTTTT
TAAAGTGCTATACCTCCAACCCTATCATAGATGTTAACTGGTTACTTTGCAAGCTAATCTTCTTG
ATGCAGCTCATAAAGGTTAATCACTTTAATTCAGTTTCTTCCTAGCCACAGTTCTTGTAACTTTG
TAAAATTTTGCAAATTTTCCATCACCTAAGATACCAAGATCAGTGAAAGCAATTCACAAATTAGA
CCATGCTCAAGAAATTACTAATAACTGACCAATCTTACCCCCTACTTCAATACTGAAACAAAAAT
TGACAAAAAGCTTGATAGGT
Found at i:29696611 original size:19 final size:20
Alignment explanation
Indices: 29696570--29696613 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
29696560 AAATGGAGAA
29696570 AAGAAAAGAAACGTAAAGAG
1 AAGAAAAGAAACGTAAAGAG
*
29696590 AAGAAAAGAAACGT-ACGAG
1 AAGAAAAGAAACGTAAAGAG
29696609 AAGAA
1 AAGAA
29696614 GAAGCAGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.64, C:0.07, G:0.25, T:0.05
Consensus pattern (20 bp):
AAGAAAAGAAACGTAAAGAG
Found at i:29696617 original size:25 final size:21
Alignment explanation
Indices: 29696566--29696616 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
29696556 GATAAAATGG
29696566 AGAA-AAGAAAAGAAACGTAA
1 AGAAGAAGAAAAGAAACGTAA
*
29696586 AG-AGAAGAAAAGAAACGTACG
1 AGAAGAAGAAAAGAAACGTA-A
29696607 AGAAGAAGAA
1 AGAAGAAGAA
29696617 GCAGAAATCG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
19 1 0.04
20 17 0.63
21 2 0.07
22 7 0.26
ACGTcount: A:0.65, C:0.06, G:0.25, T:0.04
Consensus pattern (21 bp):
AGAAGAAGAAAAGAAACGTAA
Found at i:29701989 original size:6 final size:6
Alignment explanation
Indices: 29701978--29702007 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
29701968 TATCATTTTT
29701978 CATTTC CATTTC CATTTC CATTTC CATTTC
1 CATTTC CATTTC CATTTC CATTTC CATTTC
29702008 TCATACCATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.33, G:0.00, T:0.50
Consensus pattern (6 bp):
CATTTC
Found at i:29702016 original size:18 final size:18
Alignment explanation
Indices: 29701978--29702028 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
29701968 TATCATTTTT
*
29701978 CATTTCCATTTCCATTTC
1 CATTTCCATTTCCATTAC
29701996 CATTTCCATTTCTCA-TAC
1 CATTTCCATTTC-CATTAC
*
29702014 CA-TACCATTT-CATTA
1 CATTTCCATTTCCATTA
29702029 TCAATTATAG
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
15 2 0.07
16 2 0.07
17 7 0.24
18 16 0.55
19 2 0.07
ACGTcount: A:0.24, C:0.31, G:0.00, T:0.45
Consensus pattern (18 bp):
CATTTCCATTTCCATTAC
Found at i:29702407 original size:5 final size:5
Alignment explanation
Indices: 29702393--29702457 Score: 57
Period size: 5 Copynumber: 13.2 Consensus size: 5
29702383 TCACATTTAT
* *
29702393 ATTCA TTTCA ATTCA AAT-A A-TCA ATTCA ATTC- ATTCA A-TCA ACTTCTA
1 ATTCA ATTCA ATTCA ATTCA ATTCA ATTCA ATTCA ATTCA ATTCA A-TTC-A
29702441 ATTCA ATTCA ATGTCA A
1 ATTCA ATTCA AT-TCA A
29702458 AGTGCCAAAT
Statistics
Matches: 50, Mismatches: 3, Indels: 13
0.76 0.05 0.20
Matches are distributed among these distances:
3 1 0.02
4 12 0.24
5 26 0.52
6 9 0.18
7 2 0.04
ACGTcount: A:0.40, C:0.20, G:0.02, T:0.38
Consensus pattern (5 bp):
ATTCA
Found at i:29703094 original size:17 final size:17
Alignment explanation
Indices: 29703052--29703098 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
29703042 AATTCAATTT
*
29703052 TAATATAAAT-AGTCAA
1 TAATATAAATAATTCAA
29703068 T-ATGACTAAATAATTCAA
1 TAAT-A-TAAATAATTCAA
29703086 TAATATAAATAAT
1 TAATATAAATAAT
29703099 ATAAAATGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
15 2 0.08
16 2 0.08
17 13 0.50
18 7 0.27
19 2 0.08
ACGTcount: A:0.55, C:0.06, G:0.04, T:0.34
Consensus pattern (17 bp):
TAATATAAATAATTCAA
Found at i:29703398 original size:30 final size:31
Alignment explanation
Indices: 29703359--29703418 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
29703349 GGAGGTGGGA
* *
29703359 TGGGAAGGGAATACAAGTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
* *
29703390 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAA
29703419 TAAAAGGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.38, C:0.02, G:0.40, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
Found at i:29703643 original size:9 final size:9
Alignment explanation
Indices: 29703626--29703662 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
29703616 TATAGTTTGA
*
29703626 TATTAGAAT
1 TATTCGAAT
29703635 TATTCGAAT
1 TATTCGAAT
*
29703644 TATTCGAGT
1 TATTCGAAT
29703653 TATTCGAAT
1 TATTCGAAT
29703662 T
1 T
29703663 CTAAAACTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.32, C:0.08, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:29707291 original size:18 final size:18
Alignment explanation
Indices: 29707253--29707297 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
29707243 ATTATTATAA
*
29707253 TATAATATATATACTTAT
1 TATAATATATATAATTAT
29707271 TATAATATATATTAATT-T
1 TATAATATATA-TAATTAT
29707289 TATAA-ATAT
1 TATAATATAT
29707298 CTTACCTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 4 0.16
18 17 0.68
19 4 0.16
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
TATAATATATATAATTAT
Found at i:29715398 original size:14 final size:14
Alignment explanation
Indices: 29715379--29715412 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
29715369 GTTTTGCTAT
29715379 AAAATTTAAAATTC
1 AAAATTTAAAATTC
29715393 AAAATTTAAAATTC
1 AAAATTTAAAATTC
29715407 AAAATT
1 AAAATT
29715413 CAATTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (14 bp):
AAAATTTAAAATTC
Found at i:29715413 original size:7 final size:7
Alignment explanation
Indices: 29715379--29715415 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
29715369 GTTTTGCTAT
*
29715379 AAAATTT
1 AAAATTC
29715386 AAAATTC
1 AAAATTC
*
29715393 AAAATTT
1 AAAATTC
29715400 AAAATTC
1 AAAATTC
29715407 AAAATTC
1 AAAATTC
29715414 AA
1 AA
29715416 TTTTTTTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.59, C:0.08, G:0.00, T:0.32
Consensus pattern (7 bp):
AAAATTC
Found at i:29719205 original size:24 final size:24
Alignment explanation
Indices: 29719178--29719229 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
29719168 TTAGTAAGTC
*
29719178 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
29719202 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
29719226 AAAT
1 AAAT
29719230 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:29719464 original size:16 final size:16
Alignment explanation
Indices: 29719443--29719473 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29719433 ATAAATATTG
*
29719443 CTTTTTTTTTCTTTTT
1 CTTTTTTTATCTTTTT
29719459 CTTTTTTTATCTTTT
1 CTTTTTTTATCTTTT
29719474 GAAATGTAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.84
Consensus pattern (16 bp):
CTTTTTTTATCTTTTT
Found at i:29724023 original size:20 final size:20
Alignment explanation
Indices: 29723998--29724047 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
29723988 TGGCTTAAAA
29723998 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
29724018 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
29724035 GTGGTAGTGGATT
1 TTGGTAGTGGATT
29724048 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:29728653 original size:20 final size:20
Alignment explanation
Indices: 29728628--29728677 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
29728618 TGGCTTAAAA
29728628 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
29728648 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
29728665 GTGGTAGTGGATT
1 TTGGTAGTGGATT
29728678 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:29735795 original size:26 final size:26
Alignment explanation
Indices: 29735752--29735823 Score: 101
Period size: 26 Copynumber: 2.8 Consensus size: 26
29735742 ATCTTCTCCG
*
29735752 AATTTTACCAAGGGTAAAATCGTCAA
1 AATTTTACCAAGGGTAAAATCATCAA
29735778 AATTTTACC-AGGGATAAAATCATCAA
1 AATTTTACCAAGGG-TAAAATCATCAA
* *
29735804 AACTTTACTAAGGGTAAAAT
1 AATTTTACCAAGGGTAAAAT
29735824 AGGGATGAGA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
25 4 0.10
26 33 0.80
27 4 0.10
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.28
Consensus pattern (26 bp):
AATTTTACCAAGGGTAAAATCATCAA
Found at i:29739248 original size:16 final size:17
Alignment explanation
Indices: 29739227--29739267 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
29739217 TCTCAAACAA
* *
29739227 AAATTTTAAG-TAAGTC
1 AAATTTTAAGAAAAGAC
29739243 AAA-TTTAAGAAAAGAC
1 AAATTTTAAGAAAAGAC
29739259 AAATTTTAA
1 AAATTTTAA
29739268 CCAAGCTCTC
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 6 0.29
16 10 0.48
17 5 0.24
ACGTcount: A:0.54, C:0.05, G:0.10, T:0.32
Consensus pattern (17 bp):
AAATTTTAAGAAAAGAC
Found at i:29744641 original size:15 final size:15
Alignment explanation
Indices: 29744621--29744658 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
29744611 TCTACGAGCA
29744621 TCCACATAACTTTCC
1 TCCACATAACTTTCC
29744636 TCCACATAACTTTCC
1 TCCACATAACTTTCC
29744651 TCCACATA
1 TCCACATA
29744659 CTTACTTTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.29, C:0.39, G:0.00, T:0.32
Consensus pattern (15 bp):
TCCACATAACTTTCC
Found at i:29748278 original size:79 final size:82
Alignment explanation
Indices: 29748167--29748351 Score: 220
Period size: 79 Copynumber: 2.3 Consensus size: 82
29748157 GCTACTCGTT
* * *
29748167 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAATTGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* * *
29748230 GGATTTAGTAAC-TCGCG
65 GGATATAGTAACTTAGCA
* **
29748247 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
29748310 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
29748327 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
29748352 CATCATTCAA
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
78 3 0.03
79 54 0.60
80 33 0.37
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.25
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:29748351 original size:40 final size:40
Alignment explanation
Indices: 29748148--29748351 Score: 220
Period size: 40 Copynumber: 5.1 Consensus size: 40
29748138 CGGAATTTAA
** *
29748148 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
29748188 CCGGTTATAGTAACTCGCACAATTGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
29748228 CCGGATTTAGTAACTCGCGCAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
29748267 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
29748307 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
29748347 CCGGA
1 CCGGA
29748352 CATCATTCAA
Statistics
Matches: 137, Mismatches: 20, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
38 2 0.01
39 32 0.23
40 91 0.66
41 12 0.09
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:29750711 original size:29 final size:31
Alignment explanation
Indices: 29750637--29750755 Score: 111
Period size: 31 Copynumber: 3.9 Consensus size: 31
29750627 ATTAGATCAA
** * *
29750637 AATTAAAGTTTCAAATATACATTTGAACCAC
1 AATTAAAGTTTCATGTATACAATTGCACCAC
* * *
29750668 AATTAGAGTTTCATGTTTATAATTGCACCA-
1 AATTAAAGTTTCATGTATACAATTGCACCAC
*
29750698 AATTAAAG-TTCATGTATACAATTGCA-CATTA
1 AATTAAAGTTTCATGTATACAATTGCACCA--C
*
29750729 AATCAAAGTTT-ATGTATACAATTGCAC
1 AATTAAAGTTTCATGTATACAATTGCAC
29750756 ATTAAATCAA
Statistics
Matches: 72, Mismatches: 11, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
28 2 0.03
29 16 0.22
30 7 0.10
31 45 0.62
32 2 0.03
ACGTcount: A:0.40, C:0.14, G:0.10, T:0.35
Consensus pattern (31 bp):
AATTAAAGTTTCATGTATACAATTGCACCAC
Found at i:29750744 original size:31 final size:31
Alignment explanation
Indices: 29750697--29750777 Score: 135
Period size: 31 Copynumber: 2.6 Consensus size: 31
29750687 TAATTGCACC
*
29750697 AAATTAAAGTTCATGTATACAATTGCACATT
1 AAATCAAAGTTCATGTATACAATTGCACATT
*
29750728 AAATCAAAGTTTATGTATACAATTGCACATT
1 AAATCAAAGTTCATGTATACAATTGCACATT
*
29750759 AAATCAAAGGTCATGTATA
1 AAATCAAAGTTCATGTATA
29750778 ATTTTGAAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.43, C:0.12, G:0.11, T:0.33
Consensus pattern (31 bp):
AAATCAAAGTTCATGTATACAATTGCACATT
Found at i:29751373 original size:61 final size:58
Alignment explanation
Indices: 29751308--29751424 Score: 171
Period size: 61 Copynumber: 2.0 Consensus size: 58
29751298 AAGTGATTAT
* * *
29751308 TTTAATATTAAATTTAATTTTATATTTATCTTGTAGATAAATATTCTATTAATTTAATAAA
1 TTTAATATTAAATTTAATCTAATATTTATC-T-T-GATAAATATTATATTAATTTAATAAA
*
29751369 TTTAATATTAAATTTAATCTAATATTTATCTTGATAACTATTATATTAATTTAATA
1 TTTAATATTAAATTTAATCTAATATTTATCTTGATAAATATTATATTAATTTAATA
29751425 TTAAAGTGAT
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
58 22 0.42
59 1 0.02
60 1 0.02
61 28 0.54
ACGTcount: A:0.41, C:0.04, G:0.03, T:0.52
Consensus pattern (58 bp):
TTTAATATTAAATTTAATCTAATATTTATCTTGATAAATATTATATTAATTTAATAAA
Found at i:29754277 original size:9 final size:9
Alignment explanation
Indices: 29754255--29754289 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
29754245 AAGCTTTATG
*
29754255 CTTACTTTC
1 CTTATTTTC
*
29754264 TTTATTTTC
1 CTTATTTTC
29754273 CTTATTTTC
1 CTTATTTTC
29754282 CTTATTTT
1 CTTATTTT
29754290 TATAGTATCA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.11, C:0.20, G:0.00, T:0.69
Consensus pattern (9 bp):
CTTATTTTC
Found at i:29760996 original size:28 final size:28
Alignment explanation
Indices: 29760958--29761062 Score: 102
Period size: 28 Copynumber: 3.7 Consensus size: 28
29760948 TGGTTATACA
* *
29760958 TATATTATATATATGCATGACTTTATCT
1 TATATAATATATATGCATGACTTTATAT
* *
29760986 TATATAATATATATGCATGGCTTTATTT
1 TATATAATATATATGCATGACTTTATAT
* * ** * *
29761014 TACATAGTATATATTAATGGATTTTGGTAT
1 TATATAATATATATGCAT-GACTTT-ATAT
29761044 TATATAATATATATGCATG
1 TATATAATATATATGCATG
29761063 GTTGAGTATA
Statistics
Matches: 60, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
28 39 0.65
29 5 0.08
30 16 0.27
ACGTcount: A:0.34, C:0.07, G:0.11, T:0.48
Consensus pattern (28 bp):
TATATAATATATATGCATGACTTTATAT
Found at i:29762200 original size:68 final size:68
Alignment explanation
Indices: 29762116--29762243 Score: 238
Period size: 68 Copynumber: 1.9 Consensus size: 68
29762106 GAATTATTAT
* *
29762116 ATTGTATGAACTGTTATTTCATATGAACAGATATTTTATTCAATTGATAATTTATGTGATCTGGC
1 ATTGTATGAACTGTTATTTCATATGAACAAATATTTTATTCAATTGATAATTTATATGATCTGGC
29762181 TAA
66 TAA
29762184 ATTGTATGAACTGTTATTTCATATGAACAAATATTTTATTCAATTGATAATTTATATGAT
1 ATTGTATGAACTGTTATTTCATATGAACAAATATTTTATTCAATTGATAATTTATATGAT
29762244 ATGCTAATTA
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 58 1.00
ACGTcount: A:0.34, C:0.08, G:0.12, T:0.45
Consensus pattern (68 bp):
ATTGTATGAACTGTTATTTCATATGAACAAATATTTTATTCAATTGATAATTTATATGATCTGGC
TAA
Found at i:29763865 original size:19 final size:20
Alignment explanation
Indices: 29763818--29763867 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
29763808 TTTGTTAAAT
*
29763818 AATAATTTAATATTTTACTTA
1 AATAATATAATATTTTAC-TA
29763839 AAT-A-ATAATATTTTA-TA
1 AATAATATAATATTTTACTA
29763856 AATAATATAATA
1 AATAATATAATA
29763868 ATATATATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 5 0.19
18 1 0.04
19 16 0.62
20 1 0.04
21 3 0.12
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (20 bp):
AATAATATAATATTTTACTA
Found at i:29765957 original size:31 final size:29
Alignment explanation
Indices: 29765881--29765957 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 29
29765871 AATATCAAAC
*
29765881 TAAAATTTTATATATAAAATTTCATAAAAT
1 TAAAA-TTTATATATAAAATTACATAAAAT
* * *
29765911 TAAAATTAATGTATAAAATTACATATTATAT
1 TAAAATTTATATATAAAATTACATA--AAAT
29765942 TAAAATTTATATATAA
1 TAAAATTTATATATAA
29765958 TTTAAGTTCC
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
29 17 0.44
30 5 0.13
31 17 0.44
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (29 bp):
TAAAATTTATATATAAAATTACATAAAAT
Found at i:29774434 original size:14 final size:14
Alignment explanation
Indices: 29774415--29774454 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
29774405 TTGATTGCAA
29774415 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
29774429 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
29774443 GGAAAATGTTTT
1 GTAAAATGTTTT
29774455 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:29774463 original size:20 final size:20
Alignment explanation
Indices: 29774438--29774477 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
29774428 CGTAAAATGA
*
29774438 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
29774458 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
29774478 GAAAAATATT
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:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:29774467 original size:34 final size:35
Alignment explanation
Indices: 29774423--29774489 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
29774413 AAGTAAAATG
* *
29774423 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGAAAAATATTTTAC
*
29774457 TTTTCTGTAAAATGATTTACTGAAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGAAAAATATTTT
29774490 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGAAAAATATTTTAC
Found at i:29774848 original size:26 final size:26
Alignment explanation
Indices: 29774815--29774872 Score: 107
Period size: 26 Copynumber: 2.2 Consensus size: 26
29774805 ATATCAAAAT
29774815 TTATAGAGACCAATTTAAAATCTAGA
1 TTATAGAGACCAATTTAAAATCTAGA
*
29774841 TTATAGAGACCAATTTAATATCTAGA
1 TTATAGAGACCAATTTAAAATCTAGA
29774867 TTATAG
1 TTATAG
29774873 TTTGAGGATG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.34
Consensus pattern (26 bp):
TTATAGAGACCAATTTAAAATCTAGA
Found at i:29776967 original size:27 final size:27
Alignment explanation
Indices: 29776929--29777027 Score: 96
Period size: 27 Copynumber: 3.6 Consensus size: 27
29776919 AAATCTTTCT
29776929 AACTATGGACAAGAAACCGATTCACAA
1 AACTATGGACAAGAAACCGATTCACAA
* * *
29776956 AACTATGGACAAGAAACCAATAACATAAA
1 AACTATGGACAAGAAACCGAT-TCA-CAA
*
29776985 GGAACTA---ACCCAGAAACCGATTCACAA
1 --AACTATGGA-CAAGAAACCGATTCACAA
29777012 AACTATGGACAAGAAA
1 AACTATGGACAAGAAA
29777028 ATATACCTTT
Statistics
Matches: 56, Mismatches: 8, Indels: 16
0.70 0.10 0.20
Matches are distributed among these distances:
25 5 0.09
27 28 0.50
28 6 0.11
29 12 0.21
31 5 0.09
ACGTcount: A:0.52, C:0.21, G:0.14, T:0.13
Consensus pattern (27 bp):
AACTATGGACAAGAAACCGATTCACAA
Found at i:29777460 original size:14 final size:14
Alignment explanation
Indices: 29777438--29777468 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
29777428 CACTGGAAAA
*
29777438 TCCGTAAAATATTT
1 TCCGGAAAATATTT
29777452 TCCGGAAAATATTT
1 TCCGGAAAATATTT
29777466 TCC
1 TCC
29777469 ACCAATCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.32, C:0.19, G:0.10, T:0.39
Consensus pattern (14 bp):
TCCGGAAAATATTT
Found at i:29783170 original size:12 final size:12
Alignment explanation
Indices: 29783140--29783171 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
29783130 TAAATTTAAT
*
29783140 TTAATACTTATC
1 TTAATAGTTATC
29783152 TTAATAGTTATC
1 TTAATAGTTATC
29783164 TTAATAGT
1 TTAATAGT
29783172 ATTATATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.34, C:0.09, G:0.06, T:0.50
Consensus pattern (12 bp):
TTAATAGTTATC
Found at i:29783200 original size:25 final size:26
Alignment explanation
Indices: 29783147--29783212 Score: 66
Period size: 25 Copynumber: 2.6 Consensus size: 26
29783137 AATTTAATAC
* *
29783147 TTATCTTAATAGTT-ATCTTAATAGTA
1 TTATATTAATA-TTAATATTAATAGTA
29783173 TTATATTAAT-TTAATATTAA-AGTGA
1 TTATATTAATATTAATATTAATAGT-A
*
29783198 TTATCTTAATATTAA
1 TTATATTAATATTAA
29783213 ATTTACTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
24 5 0.15
25 16 0.47
26 13 0.38
ACGTcount: A:0.39, C:0.05, G:0.06, T:0.50
Consensus pattern (26 bp):
TTATATTAATATTAATATTAATAGTA
Found at i:29783278 original size:11 final size:11
Alignment explanation
Indices: 29783248--29783282 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
29783238 ATAAATATTC
29783248 TATTAATTTAA
1 TATTAATTTAA
*
29783259 TA-AAATTTAA
1 TATTAATTTAA
29783269 TATTAATTTAA
1 TATTAATTTAA
29783280 TAT
1 TAT
29783283 AATACTTATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (11 bp):
TATTAATTTAA
Found at i:29783285 original size:10 final size:10
Alignment explanation
Indices: 29783251--29783285 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
29783241 AATATTCTAT
29783251 TAATTTAATA
1 TAATTTAATA
*
29783261 AAATTTAATA
1 TAATTTAATA
29783271 TTAATTTAATA
1 -TAATTTAATA
29783282 TAAT
1 TAAT
29783286 ACTTATCTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (10 bp):
TAATTTAATA
Found at i:29784812 original size:17 final size:17
Alignment explanation
Indices: 29784782--29784816 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
29784772 AATATGGAAA
*
29784782 GTAATCTTAAAAGATTT
1 GTAATATTAAAAGATTT
*
29784799 GTAATATTATAAGATTT
1 GTAATATTAAAAGATTT
29784816 G
1 G
29784817 ATTTTGTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.40, C:0.03, G:0.14, T:0.43
Consensus pattern (17 bp):
GTAATATTAAAAGATTT
Found at i:29786152 original size:25 final size:26
Alignment explanation
Indices: 29786116--29786164 Score: 75
Period size: 25 Copynumber: 1.9 Consensus size: 26
29786106 CGCTCAATTT
29786116 ATTTCTAGTATTTATTTT-TATTTGA
1 ATTTCTAGTATTTATTTTATATTTGA
29786141 ATTT-TAGTTATTTATTTTATATTT
1 ATTTCTAG-TATTTATTTTATATTT
29786165 AGATTTAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 3 0.14
25 14 0.64
26 5 0.23
ACGTcount: A:0.24, C:0.02, G:0.06, T:0.67
Consensus pattern (26 bp):
ATTTCTAGTATTTATTTTATATTTGA
Found at i:29786165 original size:19 final size:19
Alignment explanation
Indices: 29786112--29786166 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 19
29786102 ATTGCGCTCA
29786112 ATTTATTTCTAGTATTTA-TT
1 ATTTATTT-TA-TATTTAGTT
*
29786132 -TTTATTTGA-ATTTTAGTT
1 ATTTATTTTATA-TTTAGTT
29786150 ATTTATTTTATATTTAG
1 ATTTATTTTATATTTAG
29786167 ATTTAATCTC
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
16 1 0.03
17 4 0.14
18 3 0.10
19 20 0.69
20 1 0.03
ACGTcount: A:0.25, C:0.02, G:0.07, T:0.65
Consensus pattern (19 bp):
ATTTATTTTATATTTAGTT
Found at i:29787778 original size:20 final size:20
Alignment explanation
Indices: 29787753--29787790 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
29787743 GTCCTTTGCC
29787753 TATTTT-TTATTTTTATTTGT
1 TATTTTATTA-TTTTATTTGT
29787773 TATTTTATTATTTTATTT
1 TATTTTATTATTTTATTT
29787791 TATTATTTCC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (20 bp):
TATTTTATTATTTTATTTGT
Found at i:29787796 original size:21 final size:20
Alignment explanation
Indices: 29787753--29787798 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
29787743 GTCCTTTGCC
*
29787753 TATTTTTTATTTTTATTTGT
1 TATTTTTTATTTTTATTTAT
29787773 TATTTTATTA-TTTTATTTTAT
1 TATTTT-TTATTTTTA-TTTAT
29787794 TATTT
1 TATTT
29787799 CCAGCACTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (20 bp):
TATTTTTTATTTTTATTTAT
Found at i:29787798 original size:13 final size:12
Alignment explanation
Indices: 29787753--29787794 Score: 57
Period size: 13 Copynumber: 3.3 Consensus size: 12
29787743 GTCCTTTGCC
29787753 TATTTTTTATTTT
1 TATTTTTTA-TTT
*
29787766 TATTTGTTATTT
1 TATTTTTTATTT
29787778 TATTATTTTATTT
1 TATT-TTTTATTT
29787791 TATT
1 TATT
29787795 ATTTCCAGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
12 7 0.27
13 19 0.73
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (12 bp):
TATTTTTTATTT
Found at i:29789590 original size:24 final size:24
Alignment explanation
Indices: 29789558--29789606 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
29789548 AAATAGTTCA
29789558 AAAAAGATATTTTTTGTTTACTAG
1 AAAAAGATATTTTTTGTTTACTAG
29789582 AAAAAGATATTTTTTGTTTACTAG
1 AAAAAGATATTTTTTGTTTACTAG
29789606 A
1 A
29789607 TTTTTCTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.39, C:0.04, G:0.12, T:0.45
Consensus pattern (24 bp):
AAAAAGATATTTTTTGTTTACTAG
Found at i:29797798 original size:13 final size:13
Alignment explanation
Indices: 29797780--29797809 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
29797770 TCTTAATTAA
*
29797780 TATTATATGATAT
1 TATTATAGGATAT
29797793 TATTATAGGATAT
1 TATTATAGGATAT
29797806 TATT
1 TATT
29797810 TTTTAGTAAT
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:0.00, G:0.10, T:0.53
Consensus pattern (13 bp):
TATTATAGGATAT
Found at i:29797959 original size:39 final size:39
Alignment explanation
Indices: 29797915--29797993 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
29797905 TTATGGCATA
29797915 TGAGTAAGGTTTTTTACACAATTTTTTCTTTCATTATTC
1 TGAGTAAGGTTTTTTACACAATTTTTTCTTTCATTATTC
29797954 TGAGTAAGGTTTTTTACACAATTTTTTCTTTCATTATTC
1 TGAGTAAGGTTTTTTACACAATTTTTTCTTTCATTATTC
29797993 T
1 T
29797994 AAATGGCTAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.23, C:0.13, G:0.10, T:0.54
Consensus pattern (39 bp):
TGAGTAAGGTTTTTTACACAATTTTTTCTTTCATTATTC
Found at i:29800565 original size:45 final size:44
Alignment explanation
Indices: 29800370--29800585 Score: 166
Period size: 45 Copynumber: 4.8 Consensus size: 44
29800360 TATTTAAACC
* * * *
29800370 GAAATAATAAGACCATAGTTGAAAGATATTATGGCACTAAACCA
1 GAAATGATAAGACCATAGTTGAAAGATACTATGGCACTAAATCG
* * *
29800414 AAAATGTGTAAGACCATAGTTGAAAGATACTATGGCATTAAAGTC-
1 GAAATG-ATAAGACCATAGTTGAAAGATACTATGGCACTAAA-TCG
* * * * *
29800459 -AATATGAACAAGACCATAGTTGAAAGATATTAGGGCATTACATCG
1 GAA-ATG-ATAAGACCATAGTTGAAAGATACTATGGCACTAAATCG
* * * ** *
29800504 GTAACGATCAAAACCATAGTTGAAAGATACTATGGCACTATTTTG
1 GAAATGAT-AAGACCATAGTTGAAAGATACTATGGCACTAAATCG
* * * *
29800549 GGAATGCATAAGACCATGGTTGGAAGATACCATGGCA
1 GAAATG-ATAAGACCATAGTTGAAAGATACTATGGCA
29800586 TCCTTTGGAA
Statistics
Matches: 137, Mismatches: 28, Indels: 13
0.77 0.16 0.07
Matches are distributed among these distances:
44 9 0.07
45 124 0.91
46 4 0.03
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.25
Consensus pattern (44 bp):
GAAATGATAAGACCATAGTTGAAAGATACTATGGCACTAAATCG
Found at i:29801698 original size:19 final size:20
Alignment explanation
Indices: 29801659--29801696 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
29801649 TGTGACCCTG
29801659 TTTCTAATTTTTTTCAAAAT
1 TTTCTAATTTTTTTCAAAAT
29801679 TTTCT-ATTTTATTTCAAA
1 TTTCTAATTTT-TTTCAAA
29801697 TTAGTCCCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.29, C:0.11, G:0.00, T:0.61
Consensus pattern (20 bp):
TTTCTAATTTTTTTCAAAAT
Found at i:29802029 original size:56 final size:56
Alignment explanation
Indices: 29801965--29802084 Score: 161
Period size: 56 Copynumber: 2.2 Consensus size: 56
29801955 GGTGTTAGGG
* *
29801965 TATTATTATGGGATACTATCTTTTAACAATTTGATTCCTAATAAGATGTTATATAA
1 TATTATTATGGGATACTATCTCTTAACAATTTGATTCCTAATAAGATATTATATAA
* * * ** *
29802021 TATTATTATGTGATATTATCTCTTAGCAATTTGATTCCTAATGGGATATTATATGA
1 TATTATTATGGGATACTATCTCTTAACAATTTGATTCCTAATAAGATATTATATAA
29802077 TA-TATTAT
1 TATTATTAT
29802085 CTTTTAGCAA
Statistics
Matches: 56, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
55 6 0.11
56 50 0.89
ACGTcount: A:0.33, C:0.08, G:0.12, T:0.47
Consensus pattern (56 bp):
TATTATTATGGGATACTATCTCTTAACAATTTGATTCCTAATAAGATATTATATAA
Found at i:29803606 original size:9 final size:9
Alignment explanation
Indices: 29803589--29803625 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
29803579 TGAGTTTTCG
29803589 AATTCGAAT
1 AATTCGAAT
*
29803598 AACTCGAAT
1 AATTCGAAT
29803607 AATTCGAAT
1 AATTCGAAT
29803616 AATTCGAAT
1 AATTCGAAT
29803625 A
1 A
29803626 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:29803702 original size:21 final size:21
Alignment explanation
Indices: 29803663--29803703 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
29803653 CCCAAACTCC
*
29803663 CAAAACTTTTTACTTTTCCCT
1 CAAAACTTTTTACTCTTCCCT
29803684 CAAAAC-TTTTACTCCTTCCC
1 CAAAACTTTTTACT-CTTCCC
29803704 ATTTTCCCCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.24, C:0.34, G:0.00, T:0.41
Consensus pattern (21 bp):
CAAAACTTTTTACTCTTCCCT
Found at i:29810040 original size:23 final size:25
Alignment explanation
Indices: 29809986--29810040 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 25
29809976 TTCAAATAGC
*
29809986 AATATTAAAATCATTACATTTGAAAT
1 AATATTAAAATCATTAAATTT-AAAT
*
29810012 AATATTAAAAT-ATTAAATTT-TAT
1 AATATTAAAATCATTAAATTTAAAT
29810035 AATATT
1 AATATT
29810041 GCTAAAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 8 0.30
25 8 0.30
26 11 0.41
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.44
Consensus pattern (25 bp):
AATATTAAAATCATTAAATTTAAAT
Found at i:29811432 original size:30 final size:30
Alignment explanation
Indices: 29811396--29811480 Score: 161
Period size: 30 Copynumber: 2.8 Consensus size: 30
29811386 ACAATATAAT
29811396 ATTAAAGACTATACTTAATTTTTAATTTAG
1 ATTAAAGACTATACTTAATTTTTAATTTAG
*
29811426 ATTAAAGGCTATACTTAATTTTTAATTTAG
1 ATTAAAGACTATACTTAATTTTTAATTTAG
29811456 ATTAAAGACTATACTTAATTTTTAA
1 ATTAAAGACTATACTTAATTTTTAA
29811481 AAATTAAAGG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 53 1.00
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.46
Consensus pattern (30 bp):
ATTAAAGACTATACTTAATTTTTAATTTAG
Found at i:29825787 original size:10 final size:10
Alignment explanation
Indices: 29825754--29825781 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
29825744 ATGAAGCAAT
29825754 GAAAAAAAAA
1 GAAAAAAAAA
29825764 GAAAAAAAAA
1 GAAAAAAAAA
29825774 GAAAAAAA
1 GAAAAAAA
29825782 TTGAAACCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (10 bp):
GAAAAAAAAA
Found at i:29825999 original size:17 final size:18
Alignment explanation
Indices: 29825967--29826000 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
29825957 GTTTTCTTTT
29825967 TTTGTTGCTGGTTGTTTC
1 TTTGTTGCTGGTTGTTTC
*
29825985 TTTGTTGGT-GTTGTTT
1 TTTGTTGCTGGTTGTTT
29826001 GTTTCTGTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.00, C:0.06, G:0.29, T:0.65
Consensus pattern (18 bp):
TTTGTTGCTGGTTGTTTC
Found at i:29834695 original size:14 final size:14
Alignment explanation
Indices: 29834676--29834703 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
29834666 GAGTAGAGGA
29834676 GCTCATAAGGGAGC
1 GCTCATAAGGGAGC
29834690 GCTCATAAGGGAGC
1 GCTCATAAGGGAGC
29834704 TTACTTTGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.21, G:0.36, T:0.14
Consensus pattern (14 bp):
GCTCATAAGGGAGC
Found at i:29839217 original size:31 final size:31
Alignment explanation
Indices: 29839177--29839237 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
29839167 TTATTCAAAA
29839177 GTATATGTATGCTTAGGTAGAGACCGAAAGG
1 GTATATGTATGCTTAGGTAGAGACCGAAAGG
*
29839208 GTATCTGTATGCTTAGGTAGAGACCGAAAG
1 GTATATGTATGCTTAGGTAGAGACCGAAAG
29839238 AGTGACTTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.31, C:0.11, G:0.31, T:0.26
Consensus pattern (31 bp):
GTATATGTATGCTTAGGTAGAGACCGAAAGG
Found at i:29839368 original size:19 final size:19
Alignment explanation
Indices: 29839333--29839369 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
29839323 CTTAGTTGAG
*
29839333 GATAATTAGCGACTTAATT
1 GATAATTAGAGACTTAATT
*
29839352 GATAATTAGAGATTTAAT
1 GATAATTAGAGACTTAAT
29839370 CAATCATAGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.05, G:0.16, T:0.38
Consensus pattern (19 bp):
GATAATTAGAGACTTAATT
Found at i:29841220 original size:12 final size:11
Alignment explanation
Indices: 29841188--29841223 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
29841178 TGACTTCTTG
*
29841188 TTTAAATTTAT
1 TTTAAATTTAA
29841199 TTTAAATTTAA
1 TTTAAATTTAA
29841210 TTTAAATTTTAA
1 TTTAAA-TTTAA
29841222 TT
1 TT
29841224 GTAGTTGGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 16 0.70
12 7 0.30
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
TTTAAATTTAA
Found at i:29846064 original size:95 final size:92
Alignment explanation
Indices: 29845920--29846092 Score: 258
Period size: 95 Copynumber: 1.8 Consensus size: 92
29845910 TCAAAAAAGC
* * *
29845920 AATTAAGCTCCTGTTTTTTTTTCACTCAATTGGGTACTTGAACTTTCAAAATGCATCAAAAAT-A
1 AATTAAGCCCCTCTTTTTTTTTCACTCAATTGGGTACTTGAACTTTCAAAATACA-CAAAAATGA
29845984 CCCTCAAATCTTTTTTTAAAAAATTAAAA
65 CCCTCAAA-CTTTTTTTAAAAAATTAAAA
*
29846013 AATTAAGCCCCTACTTTTTTTTTCCACTCAATTGGGTACTTGAACTTTCAAAATACACCAAAATG
1 AATTAAGCCCCT-CTTTTTTTTT-CACTCAATTGGGTACTTGAACTTTCAAAATACACAAAAATG
*
29846078 ACTCTCAAACTTTTT
64 ACCCTCAAACTTTTT
29846093 CAAAAAAAAA
Statistics
Matches: 72, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
93 11 0.15
94 21 0.29
95 40 0.56
ACGTcount: A:0.34, C:0.20, G:0.08, T:0.38
Consensus pattern (92 bp):
AATTAAGCCCCTCTTTTTTTTTCACTCAATTGGGTACTTGAACTTTCAAAATACACAAAAATGAC
CCTCAAACTTTTTTTAAAAAATTAAAA
Found at i:29846250 original size:30 final size:29
Alignment explanation
Indices: 29846216--29846363 Score: 97
Period size: 30 Copynumber: 5.0 Consensus size: 29
29846206 TAAAAATTAG
29846216 AAAA-TATAAAAATCGTAAAAAAATATAAAA
1 AAAATTATAAAAAT-GTAAAAAAATAT-AAA
* * * *
29846246 AAAATTGTAAAATTTTATAAAAATTATAAA
1 AAAATTATAAAAATGTA-AAAAAATATAAA
***
29846276 AAAATTATAAAATAT-T-TTGAAATATAAA
1 AAAATTATAAAA-ATGTAAAAAAATATAAA
* * * *
29846304 AAAGTTAT-AAAATCATAAGAAAATCATAAG
1 AAAATTATAAAAAT-GTAAAAAAAT-ATAAA
*
29846334 AAAATTATACAAAATGTAAAGAAATATAAA
1 AAAATTATA-AAAATGTAAAAAAATATAAA
29846364 TTTCGTAAAT
Statistics
Matches: 89, Mismatches: 20, Indels: 18
0.70 0.16 0.14
Matches are distributed among these distances:
26 2 0.02
27 3 0.03
28 16 0.18
29 4 0.04
30 36 0.40
31 23 0.26
32 5 0.06
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.28
Consensus pattern (29 bp):
AAAATTATAAAAATGTAAAAAAATATAAA
Found at i:29846257 original size:10 final size:10
Alignment explanation
Indices: 29846233--29846348 Score: 55
Period size: 11 Copynumber: 11.7 Consensus size: 10
29846223 AAAAATCGTA
*
29846233 AAAAAATATAA
1 AAAAAAT-TAT
*
29846244 AAAAAATTGT
1 AAAAAATTAT
**
29846254 AAAATTTTAT
1 AAAAAATTAT
29846264 -AAAAATTAT
1 AAAAAATTAT
29846273 AAAAAAATTAT
1 -AAAAAATTAT
*
29846284 AAAATATT-T
1 AAAAAATTAT
**
29846293 -TGAAA-TAT
1 AAAAAATTAT
29846301 AAAAAAGTTAT
1 AAAAAA-TTAT
*
29846312 --AAAATCAT
1 AAAAAATTAT
*
29846320 AAGAAAATCAT
1 AA-AAAATTAT
29846331 AAGAAAATTAT
1 AA-AAAATTAT
*
29846342 ACAAAAT
1 AAAAAAT
29846349 GTAAAGAAAT
Statistics
Matches: 80, Mismatches: 16, Indels: 19
0.70 0.14 0.17
Matches are distributed among these distances:
7 1 0.01
8 6 0.08
9 15 0.19
10 20 0.25
11 38 0.47
ACGTcount: A:0.64, C:0.03, G:0.04, T:0.29
Consensus pattern (10 bp):
AAAAAATTAT
Found at i:29846277 original size:20 final size:19
Alignment explanation
Indices: 29846199--29846348 Score: 53
Period size: 19 Copynumber: 7.7 Consensus size: 19
29846189 AATAAAAAAT
* *
29846199 AAATTATTAAAAATTA-GA
1 AAATTATAAAAAATTATAA
*
29846217 AAA-TAT-AAAAATCGTAAAA
1 AAATTATAAAAAAT--TATAA
* *
29846236 AAATATAAAAAAAATTGT-A
1 AAAT-TATAAAAAATTATAA
*
29846255 AAATTTTATAAAAATTATAAAA
1 AAATTATA-AAAAATTAT--AA
* **
29846277 AAATTATAAAATATT-TTG
1 AAATTATAAAAAATTATAA
29846295 AAA-TATAAAAAAGTTAT-A
1 AAATTATAAAAAA-TTATAA
* *
29846313 AAATCATAAGAAAATCATAAGA
1 AAATTATAA-AAAATTAT-A-A
*
29846335 AAATTATACAAAAT
1 AAATTATAAAAAAT
29846349 GTAAAGAAAT
Statistics
Matches: 98, Mismatches: 17, Indels: 31
0.67 0.12 0.21
Matches are distributed among these distances:
16 6 0.06
17 11 0.11
18 15 0.15
19 25 0.26
20 6 0.06
21 13 0.13
22 22 0.22
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (19 bp):
AAATTATAAAAAATTATAA
Found at i:29846325 original size:28 final size:26
Alignment explanation
Indices: 29846261--29846363 Score: 73
Period size: 28 Copynumber: 3.6 Consensus size: 26
29846251 TGTAAAATTT
29846261 TATAA-AAATTATAAAAAAATTATAAAA
1 TATAAGAAA-TAT-AAAAAATTATAAAA
**
29846288 TATTTTGAAATATAAAAAAGTTATAAAA
1 TA-TAAGAAATATAAAAAA-TTATAAAA
29846316 TCATAAGAAAATCATAAGAAAATTATACAAAA
1 T-ATAAG-AAAT-ATAA-AAAATTAT--AAAA
*
29846348 TGTAAAGAAATATAAA
1 TAT-AAGAAATATAAA
29846364 TTTCGTAAAT
Statistics
Matches: 61, Mismatches: 5, Indels: 18
0.73 0.06 0.21
Matches are distributed among these distances:
27 8 0.13
28 15 0.25
29 9 0.15
30 12 0.20
31 9 0.15
32 8 0.13
ACGTcount: A:0.63, C:0.03, G:0.06, T:0.28
Consensus pattern (26 bp):
TATAAGAAATATAAAAAATTATAAAA
Found at i:29846742 original size:86 final size:88
Alignment explanation
Indices: 29846590--29846778 Score: 199
Period size: 86 Copynumber: 2.2 Consensus size: 88
29846580 AGAGCAGGGG
* * **
29846590 CTTAATTGC-TTTTTTGAAAAATTTTGAGGGTCTTTTTGATGTATTTGGAAAGTTCAAATATCCA
1 CTTAATTGCTTTTTTTGAAAAAGTTTAAGGGTCTTTTTGATACATTTGGAAAGTTCAAATATCCA
* * *
29846654 ATTGATTGAAAAAAGT-AAGG-A
66 ATTGAGTAAAAAAAATGAAGGAA
* * * * *
29846675 CTTAATTGCTTTTTTTGAAGAAGTTTAAGGGT-TGTTTTGATACATTTTGAAAGTTTAAGT-GCT
1 CTTAATTGCTTTTTTTGAAAAAGTTTAAGGGTCT-TTTTGATACATTTGGAAAGTTCAAATATC-
*
29846738 CAATTGAGTAAAAAAAATGGAGGAA
64 CAATTGAGTAAAAAAAATGAAGGAA
*
29846763 CTTAATTGTTTTTTTT
1 CTTAATTGCTTTTTTT
29846779 TTTTTTTAAG
Statistics
Matches: 85, Mismatches: 14, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
85 11 0.13
86 55 0.65
87 3 0.04
88 16 0.19
ACGTcount: A:0.32, C:0.06, G:0.19, T:0.42
Consensus pattern (88 bp):
CTTAATTGCTTTTTTTGAAAAAGTTTAAGGGTCTTTTTGATACATTTGGAAAGTTCAAATATCCA
ATTGAGTAAAAAAAATGAAGGAA
Found at i:29847394 original size:17 final size:17
Alignment explanation
Indices: 29847362--29847411 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
29847352 ATTTTGAAAA
29847362 AAAATTAAATATATATTTT
1 AAAATT-AA-ATATATTTT
29847381 AAAATTAAATATATTTT
1 AAAATTAAATATATTTT
*
29847398 -AATTTAAA-ATATTT
1 AAAATTAAATATATTT
29847412 AATTTTTTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
15 6 0.20
16 7 0.23
17 9 0.30
18 2 0.07
19 6 0.20
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
AAAATTAAATATATTTT
Found at i:29847414 original size:14 final size:16
Alignment explanation
Indices: 29847372--29847416 Score: 58
Period size: 17 Copynumber: 2.9 Consensus size: 16
29847362 AAAATTAAAT
*
29847372 ATATATTTTAAAATTAA
1 ATATATTTT-AATTTAA
29847389 ATATATTTTAATTTAA
1 ATATATTTTAATTTAA
29847405 A-ATA-TTTAATTT
1 ATATATTTTAATTT
29847417 TTTAATTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 8 0.30
15 3 0.11
16 7 0.26
17 9 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATATATTTTAATTTAA
Found at i:29855335 original size:16 final size:15
Alignment explanation
Indices: 29855314--29855344 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
29855304 TTTTTAAAAA
29855314 ATAAAAATAGAAAATT
1 ATAAAAAT-GAAAATT
29855330 ATAAAAATGAAAATT
1 ATAAAAATGAAAATT
29855345 TTAAGAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (15 bp):
ATAAAAATGAAAATT
Found at i:29858685 original size:51 final size:51
Alignment explanation
Indices: 29858555--29858889 Score: 288
Period size: 51 Copynumber: 6.6 Consensus size: 51
29858545 AGTTGCTAGG
* * * *
29858555 TCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTACCGGA-ATG-ATAGG
1 TCACATGTGTAGTACTATGTGTAGGCTACTACGTGTACCGGATA-GCTTCGA
** ***
29858605 TTGCATGTGTAGTACTATGTGTAGGCTACTATACGTACCGGATAGCTTCGA
1 TCACATGTGTAGTACTATGTGTAGGCTACTACGTGTACCGGATAGCTTCGA
* * * *** *
29858656 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGAAAAT-GG
1 TCACATGTGTAGTACTATGTGTAGGCTACTACGTGTACCGGAT-AGCTTCGA
* * * *
29858707 TCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTACC-GAAATGAC--AGG
1 TCACATGTGTAGTACTATGTGTAGGCTACTACGTGTACCGGATA-G-CTTCGA
* * *
29858757 TCGCATGTGTAGTACTATGTGTAGGCTACTATGTGTACCAGATAGCTTCGA
1 TCACATGTGTAGTACTATGTGTAGGCTACTACGTGTACCGGATAGCTTCGA
* ** *** *
29858808 TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATTGGATGAAAAT-GG
1 TCACATGTGTAGTACTATGTGTAGGCTACTACGTGTACCGGAT-AGCTTCGA
* *
29858859 TCACATGTGTAGTACTATGTGCAGTCTACTA
1 TCACATGTGTAGTACTATGTGTAGGCTACTA
29858890 TGTGAACTGG
Statistics
Matches: 232, Mismatches: 43, Indels: 19
0.79 0.15 0.06
Matches are distributed among these distances:
49 2 0.01
50 78 0.34
51 148 0.64
52 4 0.02
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (51 bp):
TCACATGTGTAGTACTATGTGTAGGCTACTACGTGTACCGGATAGCTTCGA
Found at i:29858766 original size:101 final size:100
Alignment explanation
Indices: 29858552--29858889 Score: 333
Period size: 101 Copynumber: 3.3 Consensus size: 100
29858542 TGAAGTTGCT
* * * **
29858552 AGGTCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTACCGGAATG-ATA-GGTTGCATGTGT
1 AGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGG-ATGAAAATGGTCACATGTGT
***
29858615 AGTACTATGTGTAGGCTACTATACGTACCGGAT-AGC
65 AGTACTATGTGTAGGCTACTACGTGTACCGGATGA-C
* * * * *
29858651 TTCGATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGAAAATGGTCACGTGTG
1 --AGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATGAAAATGGTCACATGTG
*
29858716 TAGTACTATGTGTAGGCTACTACGTGTACCGAAATGAC
64 TAGTACTATGTGTAGGCTACTACGTGTACCG-GATGAC
* * * * *** *
29858754 AGGTCGCATGTGTAGTACTATGTGTAGGCTACTATGTGTACCAGAT-AGCTTCGATCACATGTGT
1 AGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATGAAAAT-GGTCACATGTGT
* ** *
29858818 AGTACTATGTGCAGGCTACTACGTGTATTGGATGAAA
65 AGTACTATGTGTAGGCTACTACGTGTACCGGATG-AC
*
29858855 ATGGTCACATGTGTAGTACTATGTGCAGTCTACTA
1 A-GGTCACATGTGTAGTACTATGTGCAGGCTACTA
29858890 TGTGAACTGG
Statistics
Matches: 197, Mismatches: 33, Indels: 13
0.81 0.14 0.05
Matches are distributed among these distances:
100 8 0.04
101 119 0.60
102 66 0.34
103 3 0.02
104 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (100 bp):
AGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATGAAAATGGTCACATGTGTA
GTACTATGTGTAGGCTACTACGTGTACCGGATGAC
Found at i:29858778 original size:12 final size:14
Alignment explanation
Indices: 29858761--29858793 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
29858751 GACAGGTCGC
29858761 ATGTGTA-G-TACT
1 ATGTGTAGGCTACT
29858773 ATGTGTAGGCTACT
1 ATGTGTAGGCTACT
29858787 ATGTGTA
1 ATGTGTA
29858794 CCAGATAGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.37
13 1 0.05
14 11 0.58
ACGTcount: A:0.24, C:0.09, G:0.27, T:0.39
Consensus pattern (14 bp):
ATGTGTAGGCTACT
Found at i:29858829 original size:152 final size:152
Alignment explanation
Indices: 29858553--29858889 Score: 575
Period size: 152 Copynumber: 2.2 Consensus size: 152
29858543 GAAGTTGCTA
* * *
29858553 GGTCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTACCGGAATGATAGGTTGCATGTGTAGT
1 GGTCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTACCGAAATGACAGGTCGCATGTGTAGT
* *
29858618 ACTATGTGTAGGCTACTATACGTACCGGATAGCTTCGATCACGTGTGTAGTACTATGTGCAGGCT
66 ACTATGTGTAGGCTACTATACGTACCAGATAGCTTCGATCACATGTGTAGTACTATGTGCAGGCT
29858683 ACTACGTGTATCGGATGAAAAT
131 ACTACGTGTATCGGATGAAAAT
29858705 GGTCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTACCGAAATGACAGGTCGCATGTGTAGT
1 GGTCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTACCGAAATGACAGGTCGCATGTGTAGT
**
29858770 ACTATGTGTAGGCTACTATGTGTACCAGATAGCTTCGATCACATGTGTAGTACTATGTGCAGGCT
66 ACTATGTGTAGGCTACTATACGTACCAGATAGCTTCGATCACATGTGTAGTACTATGTGCAGGCT
*
29858835 ACTACGTGTATTGGATGAAAAT
131 ACTACGTGTATCGGATGAAAAT
* * *
29858857 GGTCACATGTGTAGTACTATGTGCAGTCTACTA
1 GGTCACGTGTGTAGTACTATGTGTAGGCTACTA
29858890 TGTGAACTGG
Statistics
Matches: 174, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
152 174 1.00
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (152 bp):
GGTCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTACCGAAATGACAGGTCGCATGTGTAGT
ACTATGTGTAGGCTACTATACGTACCAGATAGCTTCGATCACATGTGTAGTACTATGTGCAGGCT
ACTACGTGTATCGGATGAAAAT
Found at i:29866574 original size:12 final size:12
Alignment explanation
Indices: 29866557--29866581 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29866547 TGGTAATTCA
29866557 GGTCGGTTAACC
1 GGTCGGTTAACC
29866569 GGTCGGTTAACC
1 GGTCGGTTAACC
29866581 G
1 G
29866582 ATTGAACACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.36, T:0.24
Consensus pattern (12 bp):
GGTCGGTTAACC
Found at i:29866651 original size:17 final size:16
Alignment explanation
Indices: 29866612--29866642 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29866602 ACTCTTATTT
*
29866612 AGAATATTTGTTGTTC
1 AGAATAATTGTTGTTC
29866628 AGAATAATTGTTGTT
1 AGAATAATTGTTGTT
29866643 TGAGAATAAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.03, G:0.19, T:0.48
Consensus pattern (16 bp):
AGAATAATTGTTGTTC
Found at i:29866895 original size:16 final size:18
Alignment explanation
Indices: 29866874--29866915 Score: 54
Period size: 16 Copynumber: 2.4 Consensus size: 18
29866864 CATCACCACA
29866874 AAACAACTCT-TA-TTTG
1 AAACAACTCTCTACTTTG
29866890 AAACAAC-CTCTACTTTG
1 AAACAACTCTCTACTTTG
29866907 AGAACAACT
1 A-AACAACT
29866916 ATGTCGAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 2 0.09
16 9 0.41
17 5 0.23
18 6 0.27
ACGTcount: A:0.40, C:0.24, G:0.07, T:0.29
Consensus pattern (18 bp):
AAACAACTCTCTACTTTG
Found at i:29872179 original size:38 final size:38
Alignment explanation
Indices: 29872137--29872216 Score: 124
Period size: 38 Copynumber: 2.1 Consensus size: 38
29872127 AGATTGTTAG
* *
29872137 AAGTTCTGTGACTCAAATTCCTATTAAACATAAAATAC
1 AAGTTCTGTGACCCAAATTCCCATTAAACATAAAATAC
* *
29872175 AAGTTGTTTGACCCAAATTCCCATTAAACATAAAATAC
1 AAGTTCTGTGACCCAAATTCCCATTAAACATAAAATAC
29872213 AAGT
1 AAGT
29872217 CAAGCTGCAC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.42, C:0.19, G:0.09, T:0.30
Consensus pattern (38 bp):
AAGTTCTGTGACCCAAATTCCCATTAAACATAAAATAC
Found at i:29872683 original size:9 final size:9
Alignment explanation
Indices: 29872671--29872719 Score: 57
Period size: 9 Copynumber: 5.6 Consensus size: 9
29872661 GACTTTTAGC
29872671 ATTTTTATA
1 ATTTTTATA
29872680 ATTTTTGA-A
1 ATTTTT-ATA
*
29872689 AATTTTA-A
1 ATTTTTATA
*
29872697 ATTTTAATA
1 ATTTTTATA
29872706 ATTTTTATA
1 ATTTTTATA
29872715 ATTTT
1 ATTTT
29872720 AAAAATTCTA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
8 7 0.21
9 26 0.76
10 1 0.03
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (9 bp):
ATTTTTATA
Found at i:29872700 original size:26 final size:25
Alignment explanation
Indices: 29872671--29872722 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 25
29872661 GACTTTTAGC
*
29872671 ATTTTTATAATTTTTGAAAATTTTAA
1 ATTTTAATAATTTTT-AAAATTTTAA
*
29872697 ATTTTAATAATTTTTATAATTTTAA
1 ATTTTAATAATTTTTAAAATTTTAA
29872722 A
1 A
29872723 AATTCTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 10 0.42
26 14 0.58
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (25 bp):
ATTTTAATAATTTTTAAAATTTTAA
Found at i:29872766 original size:20 final size:18
Alignment explanation
Indices: 29872741--29872779 Score: 60
Period size: 20 Copynumber: 2.1 Consensus size: 18
29872731 TTTTAAAAAA
29872741 TATTTTAAATGATTTTCTAT
1 TATTTTAAAT-ATTTT-TAT
29872761 TATTTTAAATATTTTTAT
1 TATTTTAAATATTTTTAT
29872779 T
1 T
29872780 TTTATATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.21
19 5 0.26
20 10 0.53
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (18 bp):
TATTTTAAATATTTTTAT
Done.