Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 97880472
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: 97880472
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 192 characters in sequence are not A, C, G, or T
File 25 of 335
Found at i:9274316 original size:7 final size:7
Alignment explanation
Indices: 9274263--9274316 Score: 54
Period size: 7 Copynumber: 7.3 Consensus size: 7
9274253 ATATTAAATA
9274263 TTAAGTTT
1 TTAA-TTT
9274271 TTAAGTTT
1 TTAA-TTT
9274279 TTAAGTTT
1 TTAA-TTT
*
9274287 TTTATTT
1 TTAATTT
*
9274294 TTTATTT
1 TTAATTT
*
9274301 TTAAATT
1 TTAATTT
9274308 TTAATTT
1 TTAATTT
9274315 TT
1 TT
9274317 TTGAAGATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
7 23 0.55
8 19 0.45
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.70
Consensus pattern (7 bp):
TTAATTT
Found at i:9275511 original size:7 final size:7
Alignment explanation
Indices: 9275499--9275523 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
9275489 ATCCAAACCC
9275499 TAAAACA
1 TAAAACA
9275506 TAAAACA
1 TAAAACA
9275513 TAAAACA
1 TAAAACA
9275520 TAAA
1 TAAA
9275524 CCATGAACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.72, C:0.12, G:0.00, T:0.16
Consensus pattern (7 bp):
TAAAACA
Found at i:9276465 original size:2 final size:2
Alignment explanation
Indices: 9276453--9276482 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
9276443 GGTTGTGGGG
*
9276453 AT AT TT 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
9276483 TTGCCATTGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:9276905 original size:16 final size:16
Alignment explanation
Indices: 9276884--9276935 Score: 77
Period size: 16 Copynumber: 3.2 Consensus size: 16
9276874 ATTTTCATGT
*
9276884 TATACACATATATATA
1 TATACAAATATATATA
9276900 TATACAAATATATATA
1 TATACAAATATATATA
* *
9276916 TATATATATATATATA
1 TATACAAATATATATA
9276932 TATA
1 TATA
9276936 TATTCATATA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (16 bp):
TATACAAATATATATA
Found at i:9276944 original size:10 final size:9
Alignment explanation
Indices: 9276907--9276946 Score: 50
Period size: 8 Copynumber: 4.7 Consensus size: 9
9276897 ATATATACAA
9276907 ATATATA-T
1 ATATATATT
9276915 ATATATA-T
1 ATATATATT
9276923 ATATATA-T
1 ATATATATT
9276931 ATATATATT
1 ATATATATT
9276940 CATATAT
1 -ATATAT
9276947 TCTTCTACAC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
8 23 0.77
9 1 0.03
10 6 0.20
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (9 bp):
ATATATATT
Found at i:9276946 original size:2 final size:2
Alignment explanation
Indices: 9276891--9276938 Score: 78
Period size: 2 Copynumber: 24.0 Consensus size: 2
9276881 TGTTATACAC
* *
9276891 AT AT AT AT AT AT AC AA 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
9276933 AT AT AT
1 AT AT AT
9276939 TCATATATTC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:9282135 original size:9 final size:9
Alignment explanation
Indices: 9282108--9282179 Score: 56
Period size: 10 Copynumber: 7.6 Consensus size: 9
9282098 TTGAAACAGC
9282108 TTATAAAAA
1 TTATAAAAA
9282117 TTATATAAAA
1 TTATA-AAAA
9282127 TTATAAAAA
1 TTATAAAAA
**
9282136 TTCATACAAGC
1 TT-ATA-AAAA
9282147 TTAT-AAAA
1 TTATAAAAA
*
9282155 TTCTTAAAAA
1 TT-ATAAAAA
*
9282165 ATATAAAAAA
1 TTAT-AAAAA
9282175 TTATA
1 TTATA
9282180 TTCTAAAATA
Statistics
Matches: 49, Mismatches: 8, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
8 4 0.08
9 14 0.29
10 27 0.55
11 4 0.08
ACGTcount: A:0.58, C:0.06, G:0.01, T:0.35
Consensus pattern (9 bp):
TTATAAAAA
Found at i:9282157 original size:19 final size:20
Alignment explanation
Indices: 9282105--9282154 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
9282095 AAATTGAAAC
*
9282105 AGCTTATAAAAATT-ATATA
1 AGCTTATAAAAATTCATACA
**
9282124 AAATTATAAAAATTCATACA
1 AGCTTATAAAAATTCATACA
9282144 AGCTTATAAAA
1 AGCTTATAAAA
9282155 TTCTTAAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.56, C:0.08, G:0.04, T:0.32
Consensus pattern (20 bp):
AGCTTATAAAAATTCATACA
Found at i:9287639 original size:15 final size:16
Alignment explanation
Indices: 9287619--9287648 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
9287609 TGAAATAAAC
9287619 TAAT-AAAATAAAAAA
1 TAATAAAAATAAAAAA
9287634 TAATAAAAATAAAAA
1 TAATAAAAATAAAAA
9287649 TAAATTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (16 bp):
TAATAAAAATAAAAAA
Found at i:9289299 original size:9 final size:8
Alignment explanation
Indices: 9289273--9289298 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
9289263 CATTTGCTTC
9289273 TTCTTTTT
1 TTCTTTTT
9289281 TTCTTTTT
1 TTCTTTTT
9289289 TTCTTTTT
1 TTCTTTTT
9289297 TT
1 TT
9289299 TTAACATGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (8 bp):
TTCTTTTT
Found at i:9292886 original size:16 final size:17
Alignment explanation
Indices: 9292865--9292899 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
9292855 TAATGTCTAG
9292865 GAAAATTA-TTAATTGA
1 GAAAATTACTTAATTGA
9292881 GAAAATTATCTTAATTGA
1 GAAAATTA-CTTAATTGA
9292899 G
1 G
9292900 GGGTTAATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
18 9 0.53
ACGTcount: A:0.46, C:0.03, G:0.14, T:0.37
Consensus pattern (17 bp):
GAAAATTACTTAATTGA
Found at i:9294283 original size:42 final size:43
Alignment explanation
Indices: 9294224--9294324 Score: 143
Period size: 42 Copynumber: 2.4 Consensus size: 43
9294214 GATATGTGAT
*
9294224 TATGTGTAAGACCATAGCTAGGCTATGGCATCAATGTATGAA-
1 TATGTGTAAGACCATAGCTAGGCTATGGCATCAATATATGAAG
* * *
9294266 TATGTGTAAGACCATAGCTGGGCTATGGCATCATTATGTGAAG
1 TATGTGTAAGACCATAGCTAGGCTATGGCATCAATATATGAAG
*
9294309 T-TGTGTAATACCATAG
1 TATGTGTAAGACCATAG
9294325 TTGAACTATG
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
42 52 0.98
43 1 0.02
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.31
Consensus pattern (43 bp):
TATGTGTAAGACCATAGCTAGGCTATGGCATCAATATATGAAG
Found at i:9294334 original size:42 final size:42
Alignment explanation
Indices: 9294215--9294339 Score: 128
Period size: 42 Copynumber: 3.0 Consensus size: 42
9294205 TCGATATGTG
* * *
9294215 ATATGTGATTATGTGTAAGACCATAGCT-AGGCTATGGCATCA
1 ATATATGAATATGTGTAAGACCATAGCTGA-ACTATGGCATCA
* **
9294257 ATGTATGAATATGTGTAAGACCATAGCTGGGCTATGGCATCA
1 ATATATGAATATGTGTAAGACCATAGCTGAACTATGGCATCA
* * * *
9294299 TTATGTGAAGT-TGTGTAATACCATAGTTGAACTATGGCATC
1 ATATATGAA-TATGTGTAAGACCATAGCTGAACTATGGCATC
9294340 GAGAAAATGA
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
42 69 0.99
43 1 0.01
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.32
Consensus pattern (42 bp):
ATATATGAATATGTGTAAGACCATAGCTGAACTATGGCATCA
Found at i:9295316 original size:29 final size:30
Alignment explanation
Indices: 9295274--9295346 Score: 76
Period size: 29 Copynumber: 2.4 Consensus size: 30
9295264 CTTGAGCCAC
* * *
9295274 AATTAGAGTTTCATATGTATAATTACACA-A
1 AATTAAAG-TTCATATATAAAATTACACATA
*
9295304 AATTAAAGTTCATGTATAAAATTACACATTA
1 AATTAAAGTTCATATATAAAATTACACA-TA
*
9295335 AATCAAAGTTCA
1 AATTAAAGTTCA
9295347 CGTATAATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
29 17 0.47
30 7 0.19
31 12 0.33
ACGTcount: A:0.47, C:0.11, G:0.08, T:0.34
Consensus pattern (30 bp):
AATTAAAGTTCATATATAAAATTACACATA
Found at i:9295346 original size:31 final size:29
Alignment explanation
Indices: 9295294--9295353 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 29
9295284 TCATATGTAT
* *
9295294 AATTACACAAAATTAAAGTTCATGTATAA
1 AATTACACAAAATCAAAGTTCACGTATAA
9295323 AATTACACATTAAATCAAAGTTCACGTATAA
1 AATTACACA--AAATCAAAGTTCACGTATAA
9295354 TTTTAAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 9 0.33
31 18 0.67
ACGTcount: A:0.50, C:0.13, G:0.07, T:0.30
Consensus pattern (29 bp):
AATTACACAAAATCAAAGTTCACGTATAA
Found at i:9297377 original size:12 final size:12
Alignment explanation
Indices: 9297360--9297385 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
9297350 CTCTGAAACC
9297360 TTTTTATTTTGG
1 TTTTTATTTTGG
9297372 TTTTTATTTTGG
1 TTTTTATTTTGG
9297384 TT
1 TT
9297386 GCTTTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.00, G:0.15, T:0.77
Consensus pattern (12 bp):
TTTTTATTTTGG
Found at i:9299451 original size:2 final size:2
Alignment explanation
Indices: 9299444--9299471 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
9299434 TTTGGAATCT
9299444 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
9299472 AGTACTTCTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:9316200 original size:41 final size:41
Alignment explanation
Indices: 9316143--9316222 Score: 151
Period size: 41 Copynumber: 2.0 Consensus size: 41
9316133 GCAAAGTTAA
*
9316143 TTTTTTTTCCTTTAACCTCGAATGAATGAATCTCAAACTAC
1 TTTTTTTTCCTTTAACCTCAAATGAATGAATCTCAAACTAC
9316184 TTTTTTTTCCTTTAACCTCAAATGAATGAATCTCAAACT
1 TTTTTTTTCCTTTAACCTCAAATGAATGAATCTCAAACT
9316223 TCAAAATAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.30, C:0.21, G:0.06, T:0.42
Consensus pattern (41 bp):
TTTTTTTTCCTTTAACCTCAAATGAATGAATCTCAAACTAC
Found at i:9318395 original size:27 final size:27
Alignment explanation
Indices: 9318365--9318419 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
9318355 AAAGCTGGTG
*
9318365 CAGCAGCAGCCACCCCAGGGTTAAACC
1 CAGCAGCAGCAACCCCAGGGTTAAACC
* *
9318392 CAGCAGCAGCAACTCCAGGGTTGAACC
1 CAGCAGCAGCAACCCCAGGGTTAAACC
9318419 C
1 C
9318420 CACTCCCACT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.29, C:0.38, G:0.24, T:0.09
Consensus pattern (27 bp):
CAGCAGCAGCAACCCCAGGGTTAAACC
Found at i:9319402 original size:6 final size:6
Alignment explanation
Indices: 9319393--9319474 Score: 76
Period size: 6 Copynumber: 13.7 Consensus size: 6
9319383 CTCCTCTTCC
** * *
9319393 TCCTCT TCCTCT TCCTCT TCCTCT TCCAGT TCCACT TCCTCT TCTTCT
1 TCCTCT TCCTCT TCCTCT TCCTCT TCCTCT TCCTCT TCCTCT TCCTCT
** * *
9319441 TCAACC TCCTCT T-CTACT TCCTCT TCCACT TCCT
1 TCCTCT TCCTCT TCCT-CT TCCTCT TCCTCT TCCT
9319475 GTAGTTTCTG
Statistics
Matches: 61, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
5 2 0.03
6 57 0.93
7 2 0.03
ACGTcount: A:0.07, C:0.46, G:0.01, T:0.45
Consensus pattern (6 bp):
TCCTCT
Found at i:9331794 original size:18 final size:18
Alignment explanation
Indices: 9331760--9331795 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
9331750 AAATTTCCCT
*
9331760 TAAATAAACTCTAAAAAC
1 TAAATAAACACTAAAAAC
9331778 TAAATTAAACACTAAAAA
1 TAAA-TAAACACTAAAAA
9331796 TTATTAAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.64, C:0.14, G:0.00, T:0.22
Consensus pattern (18 bp):
TAAATAAACACTAAAAAC
Found at i:9339721 original size:22 final size:22
Alignment explanation
Indices: 9339692--9339759 Score: 75
Period size: 22 Copynumber: 3.0 Consensus size: 22
9339682 TGCACAAACG
9339692 AACAGAGAGCACTAAAGTGCTA
1 AACAGAGAGCACTAAAGTGCTA
* **
9339714 TACAGAGAGCAC-AGTTGTGCTA
1 AACAGAGAGCACTA-AAGTGCTA
*
9339736 AACAGAGAGCACTTAACGTGCTA
1 AACAGAGAGCAC-TAAAGTGCTA
9339759 A
1 A
9339760 TAATAGAATG
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
21 1 0.03
22 28 0.76
23 7 0.19
24 1 0.03
ACGTcount: A:0.40, C:0.19, G:0.24, T:0.18
Consensus pattern (22 bp):
AACAGAGAGCACTAAAGTGCTA
Found at i:9340910 original size:20 final size:20
Alignment explanation
Indices: 9340871--9340910 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
9340861 TTCGTCCCTG
* *
9340871 CTATTCTGTTTTTTTTCTTT
1 CTATTCTGTTTCTTTACTTT
*
9340891 CTATTTTGTTTCTTTACTTT
1 CTATTCTGTTTCTTTACTTT
9340911 ACTTATGTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.07, C:0.15, G:0.05, T:0.72
Consensus pattern (20 bp):
CTATTCTGTTTCTTTACTTT
Found at i:9344271 original size:15 final size:15
Alignment explanation
Indices: 9344251--9344317 Score: 68
Period size: 15 Copynumber: 4.5 Consensus size: 15
9344241 TTCTAATACT
9344251 ATTATTATTTATCTA
1 ATTATTATTTATCTA
9344266 ATTATTATTTATCTA
1 ATTATTATTTATCTA
* *
9344281 TTTA-TATTTCTACT-
1 ATTATTATTTAT-CTA
9344295 ATTATTATATT-TCTA
1 ATTATTAT-TTATCTA
*
9344310 TTTATTAT
1 ATTATTAT
9344318 ATTTTTATTT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
14 11 0.25
15 31 0.70
16 2 0.05
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (15 bp):
ATTATTATTTATCTA
Found at i:9344281 original size:29 final size:29
Alignment explanation
Indices: 9344249--9344317 Score: 72
Period size: 29 Copynumber: 2.3 Consensus size: 29
9344239 TATTCTAATA
9344249 CTATTATTATTTAT-CTAATTATTAT-TTAT
1 CTATTATTATTTATACT-ATTATTATATT-T
*
9344278 CTATT-TATATTTCTACTATTATTATATTT
1 CTATTAT-TATTTATACTATTATTATATTT
9344307 CTATTTATTAT
1 CTA-TTATTAT
9344318 ATTTTTATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
28 1 0.03
29 23 0.68
30 9 0.26
31 1 0.03
ACGTcount: A:0.29, C:0.09, G:0.00, T:0.62
Consensus pattern (29 bp):
CTATTATTATTTATACTATTATTATATTT
Found at i:9344318 original size:15 final size:15
Alignment explanation
Indices: 9344282--9344327 Score: 65
Period size: 15 Copynumber: 2.9 Consensus size: 15
9344272 ATTTATCTAT
9344282 TTATATTTCTACTATTA
1 TTATATTTCTA-T-TTA
9344299 TTATATTTCTATTTA
1 TTATATTTCTATTTA
*
9344314 TTATATTTTTATTT
1 TTATATTTCTATTT
9344328 CTATTTATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
15 16 0.57
16 1 0.04
17 11 0.39
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (15 bp):
TTATATTTCTATTTA
Found at i:9345667 original size:31 final size:32
Alignment explanation
Indices: 9345622--9345687 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 32
9345612 TTTTTTAGCT
*
9345622 AAATTTACTCATTAA-CTTCTT-AAAAAGAGTC
1 AAATTTACTCATTAATCTT-TTGAAAAAGAGCC
9345653 AAATTTGACT-ATTAATCTTTTGAAAAAGAGCC
1 AAATTT-ACTCATTAATCTTTTGAAAAAGAGCC
9345685 AAA
1 AAA
9345688 ATGATAATAC
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
31 13 0.42
32 18 0.58
ACGTcount: A:0.44, C:0.14, G:0.09, T:0.33
Consensus pattern (32 bp):
AAATTTACTCATTAATCTTTTGAAAAAGAGCC
Found at i:9348172 original size:2 final size:2
Alignment explanation
Indices: 9348165--9348193 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
9348155 CAAAGGTGCA
9348165 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
9348194 AATAATTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9352835 original size:12 final size:12
Alignment explanation
Indices: 9352818--9352842 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
9352808 TGAACTGTTG
9352818 TCAAGATTTTTC
1 TCAAGATTTTTC
9352830 TCAAGATTTTTC
1 TCAAGATTTTTC
9352842 T
1 T
9352843 AACTTCAAAC
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:0.24, C:0.16, G:0.08, T:0.52
Consensus pattern (12 bp):
TCAAGATTTTTC
Found at i:9359389 original size:5 final size:5
Alignment explanation
Indices: 9359381--9359413 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
9359371 GATTTATATA
9359381 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTT
9359414 TTTAATAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTCT
Found at i:9360596 original size:34 final size:34
Alignment explanation
Indices: 9360558--9360629 Score: 78
Period size: 35 Copynumber: 2.1 Consensus size: 34
9360548 TTATGTTTAG
9360558 TTCAC-AAAATACT-TTATTAAA-AATATAATAATAA
1 TTCACGAAAATACTCTTATTAAATAA-A-AATAAT-A
**
9360592 TTCACGAATTTACTCTTATTAAATAAAAATAATA
1 TTCACGAAAATACTCTTATTAAATAAAAATAATA
9360626 TTCA
1 TTCA
9360630 TATATTAAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
34 10 0.30
35 12 0.36
36 9 0.27
37 2 0.06
ACGTcount: A:0.50, C:0.11, G:0.01, T:0.38
Consensus pattern (34 bp):
TTCACGAAAATACTCTTATTAAATAAAAATAATA
Found at i:9363991 original size:17 final size:16
Alignment explanation
Indices: 9363969--9364014 Score: 56
Period size: 18 Copynumber: 2.7 Consensus size: 16
9363959 TATGTTTATG
*
9363969 GAAAAATAACTCTCCAA
1 GAAAAATAAAT-TCCAA
9363986 GAAAAAGTTAAATTCCAA
1 GAAAAA--TAAATTCCAA
9364004 GAAAAATAAAT
1 GAAAAATAAAT
9364015 AAAATCCGAC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 5 0.19
17 6 0.23
18 11 0.42
19 4 0.15
ACGTcount: A:0.59, C:0.13, G:0.09, T:0.20
Consensus pattern (16 bp):
GAAAAATAAATTCCAA
Found at i:9374478 original size:11 final size:11
Alignment explanation
Indices: 9374464--9374503 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
9374454 GTTTTCTCCA
9374464 TATTTTGCTAC
1 TATTTTGCTAC
* *
9374475 TATTTTACTAT
1 TATTTTGCTAC
*
9374486 TATGTTGCTAC
1 TATTTTGCTAC
9374497 TATTTTG
1 TATTTTG
9374504 TTGTTATTGT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.20, C:0.12, G:0.10, T:0.57
Consensus pattern (11 bp):
TATTTTGCTAC
Found at i:9374590 original size:29 final size:31
Alignment explanation
Indices: 9374540--9374601 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 31
9374530 ATTTATTTTC
9374540 TTGTTAATTTTTTTATTTA-TTTAAAGGCAT
1 TTGTTAATTTTTTTATTTATTTTAAAGGCAT
*
9374570 TTGTTAATTTTTTTA-TTATTTTAGAGGCAT
1 TTGTTAATTTTTTTATTTATTTTAAAGGCAT
9374600 TT
1 TT
9374602 ACTTGTTAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 3 0.10
30 27 0.90
ACGTcount: A:0.24, C:0.03, G:0.11, T:0.61
Consensus pattern (31 bp):
TTGTTAATTTTTTTATTTATTTTAAAGGCAT
Found at i:9376358 original size:2 final size:2
Alignment explanation
Indices: 9376351--9376381 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
9376341 AACCTTTAAC
9376351 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9376382 GAAACCTCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9376595 original size:51 final size:51
Alignment explanation
Indices: 9376540--9376675 Score: 166
Period size: 51 Copynumber: 2.7 Consensus size: 51
9376530 TGGAAACATG
* *
9376540 ATCTTAAAAGATATGATTTTATAATCTTAGAGATCTTAGATATGATATGTA
1 ATCTTAAAAGATATAATTTTATAATCTTAGAGATCTTAGATAAGATATGTA
* * ** * *
9376591 ATCTTATAAGATATTATTTTATAAGATT-GCATATTTTAGATAAGATATGTA
1 ATCTTAAAAGATATAATTTTATAATCTTAG-AGATCTTAGATAAGATATGTA
* *
9376642 ATCTTAGAAGATATAATTTTATATTCTTAGAGAT
1 ATCTTAAAAGATATAATTTTATAATCTTAGAGAT
9376676 TTGATTGTAG
Statistics
Matches: 70, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
50 1 0.01
51 68 0.97
52 1 0.01
ACGTcount: A:0.39, C:0.05, G:0.12, T:0.43
Consensus pattern (51 bp):
ATCTTAAAAGATATAATTTTATAATCTTAGAGATCTTAGATAAGATATGTA
Found at i:9376648 original size:19 final size:19
Alignment explanation
Indices: 9376572--9376649 Score: 62
Period size: 19 Copynumber: 4.4 Consensus size: 19
9376562 AATCTTAGAG
*
9376572 ATCTTAGATATGATATGTA
1 ATCTTAGATAAGATATGTA
9376591 ATCTT--ATAAGATAT-T-
1 ATCTTAGATAAGATATGTA
* *
9376606 AT-TT-TATAAGAT-TGCA
1 ATCTTAGATAAGATATGTA
*
9376622 TATTTTAGATAAGATATGTA
1 -ATCTTAGATAAGATATGTA
9376642 ATCTTAGA
1 ATCTTAGA
9376650 AGATATAATT
Statistics
Matches: 47, Mismatches: 5, Indels: 14
0.71 0.08 0.21
Matches are distributed among these distances:
14 3 0.06
15 9 0.19
16 1 0.02
17 10 0.21
18 2 0.04
19 19 0.40
20 3 0.06
ACGTcount: A:0.38, C:0.05, G:0.13, T:0.44
Consensus pattern (19 bp):
ATCTTAGATAAGATATGTA
Found at i:9385841 original size:21 final size:21
Alignment explanation
Indices: 9385779--9385842 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 21
9385769 GAATTCAAGT
*
9385779 TTTTATGTTATATAATAAAATA
1 TTTTATGTTAT-TAATAAAAAA
* ** *
9385801 TTTT-TATTACTGGATTAAAAA
1 TTTTATGTTA-TTAATAAAAAA
9385822 TTTTATGTTATTAATAAAAAA
1 TTTTATGTTATTAATAAAAAA
9385843 ACATTAGTTA
Statistics
Matches: 31, Mismatches: 9, Indels: 5
0.69 0.20 0.11
Matches are distributed among these distances:
21 22 0.71
22 9 0.29
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (21 bp):
TTTTATGTTATTAATAAAAAA
Found at i:9386562 original size:19 final size:18
Alignment explanation
Indices: 9386540--9386578 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
9386530 TTAATAATAT
*
9386540 AATAACGAAATAATAGTAA
1 AATAACGAAA-AAAAGTAA
*
9386559 AATAATGAAAAAAAGTAA
1 AATAACGAAAAAAAGTAA
9386577 AA
1 AA
9386579 AAAAACAGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.69, C:0.03, G:0.10, T:0.18
Consensus pattern (18 bp):
AATAACGAAAAAAAGTAA
Found at i:9391891 original size:13 final size:14
Alignment explanation
Indices: 9391873--9391901 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
9391863 TCTTCTACTC
9391873 TACTCACATG-ATT
1 TACTCACATGTATT
9391886 TACTCACATGTATT
1 TACTCACATGTATT
9391900 TA
1 TA
9391902 AGATTTCCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.31, C:0.21, G:0.07, T:0.41
Consensus pattern (14 bp):
TACTCACATGTATT
Found at i:9394029 original size:54 final size:54
Alignment explanation
Indices: 9393945--9394054 Score: 211
Period size: 54 Copynumber: 2.0 Consensus size: 54
9393935 TCACCGCCAC
*
9393945 AAATTCCTAACTCATCTAATCTCTTTTGTGACATCATTATCTAATGAGCTAATT
1 AAATTCCTAACTCATCTAATCTCTTATGTGACATCATTATCTAATGAGCTAATT
9393999 AAATTCCTAACTCATCTAATCTCTTATGTGACATCATTATCTAATGAGCTAATT
1 AAATTCCTAACTCATCTAATCTCTTATGTGACATCATTATCTAATGAGCTAATT
9394053 AA
1 AA
9394055 TTCTTTTGGG
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.34, C:0.20, G:0.07, T:0.39
Consensus pattern (54 bp):
AAATTCCTAACTCATCTAATCTCTTATGTGACATCATTATCTAATGAGCTAATT
Found at i:9400710 original size:24 final size:24
Alignment explanation
Indices: 9400678--9400727 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
9400668 CTTGAGGCAG
9400678 AAAACACCTTATGCACAATGCTGC
1 AAAACACCTTATGCACAATGCTGC
9400702 AAAACACCTTATGCACAATGCTGC
1 AAAACACCTTATGCACAATGCTGC
9400726 AA
1 AA
9400728 TTGTAATTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.40, C:0.28, G:0.12, T:0.20
Consensus pattern (24 bp):
AAAACACCTTATGCACAATGCTGC
Found at i:9401147 original size:44 final size:44
Alignment explanation
Indices: 9401084--9401172 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
9401074 AGTATGCATT
9401084 ACGCACCATCATCACAAGATGCTTGTTCTATGTTCTACAATCAA
1 ACGCACCATCATCACAAGATGCTTGTTCTATGTTCTACAATCAA
9401128 ACGCACCATCATCACAAGATGCTTGTTCTATGTTCTACAATCAA
1 ACGCACCATCATCACAAGATGCTTGTTCTATGTTCTACAATCAA
9401172 A
1 A
9401173 TCTAGCCAAC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.33, C:0.27, G:0.11, T:0.29
Consensus pattern (44 bp):
ACGCACCATCATCACAAGATGCTTGTTCTATGTTCTACAATCAA
Found at i:9403002 original size:195 final size:196
Alignment explanation
Indices: 9402671--9403061 Score: 678
Period size: 195 Copynumber: 2.0 Consensus size: 196
9402661 ACGGAGAAAC
* *
9402671 AAATTATGTTTAAAGTTAGATTTTACTCAATTTAAAATTTAATTGAAGTTTAATGTTATTATTGT
1 AAATTATGTTTAAAGTTAGATTTCACTCAATTTAAAATTTAATTGAAGTTTAATGTCATTATTGT
9402736 ATACTAAAAGGCTTTAAAAAAAATCTAATAATATAGTAATGAGTGACAAATTTTTTTAAGGGAAC
66 ATACTAAAAGGCTTTAAAAAAAATCTAATAATATAGTAATGAGTGACAAATTTTTTTAAGGGAAC
* * *
9402801 AAATAATATTTAAGGTAGAGTTTTGTTATAGTGAAATTCTGTA-GAAT-TTTTTAGGTCAATTAT
131 AAATAATATTTAAGGTAGAGTTTTATTATAGTGAAATTCTATAGGAATCTTTTTAGATCAATTAT
9402864 T
196 T
* *
9402865 AAATTATGTTTAGAGTTAAGATTTCACTCAATTTAGAATTTAATTGAAGTTTAATGTCATTATTG
1 AAATTATGTTTAAAGTT-AGATTTCACTCAATTTAAAATTTAATTGAAGTTTAATGTCATTATTG
*
9402930 TATACTAAAAGGCTTTAAAAAAACTCTAATAATATAGTAATGAGTGACAAATTTTTTTAAGGGAA
65 TATACTAAAAGGCTTTAAAAAAAATCTAATAATATAGTAATGAGTGACAAATTTTTTTAAGGGAA
*
9402995 CAAATAATATTTAAGGTGGAGTTTTATTATAGTGAAATTCTATAGGAATCTTTTTAGATCAATTA
130 CAAATAATATTTAAGGTAGAGTTTTATTATAGTGAAATTCTATAGGAATCTTTTTAGATCAATTA
9403060 TT
195 TT
9403062 GTAGTTAAGA
Statistics
Matches: 185, Mismatches: 9, Indels: 3
0.94 0.05 0.02
Matches are distributed among these distances:
194 16 0.09
195 149 0.81
196 4 0.02
197 16 0.09
ACGTcount: A:0.39, C:0.06, G:0.14, T:0.41
Consensus pattern (196 bp):
AAATTATGTTTAAAGTTAGATTTCACTCAATTTAAAATTTAATTGAAGTTTAATGTCATTATTGT
ATACTAAAAGGCTTTAAAAAAAATCTAATAATATAGTAATGAGTGACAAATTTTTTTAAGGGAAC
AAATAATATTTAAGGTAGAGTTTTATTATAGTGAAATTCTATAGGAATCTTTTTAGATCAATTAT
T
Found at i:9404595 original size:14 final size:14
Alignment explanation
Indices: 9404557--9404609 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
9404547 TCGATATCAA
* *
9404557 ATATTATAATGTTAA
1 ATATT-TAATGATAT
9404572 ATATTTTAATGATAT
1 ATA-TTTAATGATAT
* *
9404587 ATATTTAATTATTT
1 ATATTTAATGATAT
9404601 ATATTTAAT
1 ATATTTAAT
9404610 AGTACAATTA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
14 18 0.55
15 13 0.39
16 2 0.06
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.55
Consensus pattern (14 bp):
ATATTTAATGATAT
Found at i:9414533 original size:46 final size:46
Alignment explanation
Indices: 9414466--9414681 Score: 315
Period size: 46 Copynumber: 4.7 Consensus size: 46
9414456 GGCAACCTGA
9414466 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAAT
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAAT
*
9414512 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAAT
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAAT
* *
9414558 GTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGATATGAAAT
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAAT
*** * * *
9414604 GAACAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAAT
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAAT
* * * *
9414650 GAGTAAGACCATAGTTGAAAGACACTATGGCA
1 GTGTAAGACCATGGTTGAAAGATACCATGGCA
9414682 TCATGTCAAA
Statistics
Matches: 156, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 156 1.00
ACGTcount: A:0.40, C:0.15, G:0.24, T:0.21
Consensus pattern (46 bp):
GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAAT
Found at i:9414661 original size:138 final size:130
Alignment explanation
Indices: 9414416--9414681 Score: 379
Period size: 138 Copynumber: 2.0 Consensus size: 130
9414406 AGTGCGCTCT
*
9414416 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGAGTGTAAGACCATGGT
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGAGTGCAAGACCATGGT
* * * * * *
9414481 TGAAAGATACCATGGCAACCTGATATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
66 TGAAAGATACCATGGCAACATGACAGAAAATGAGTAAGACCATAGTTGAAAGACACCATGGCAAC
*
9414546 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGATATGAAATGAACAAG
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG--A-G---TG--CAAG
*
9414611 ACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAGTAAGACCATAGTTGAAAGACACT
58 ACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAGTAAGACCATAGTTGAAAGACACC
9414676 ATGGCA
123 ATGGCA
9414682 TCATGTCAAA
Statistics
Matches: 119, Mismatches: 9, Indels: 8
0.88 0.07 0.06
Matches are distributed among these distances:
130 48 0.40
132 1 0.01
133 1 0.01
136 2 0.02
138 67 0.56
ACGTcount: A:0.39, C:0.15, G:0.24, T:0.22
Consensus pattern (130 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGAGTGCAAGACCATGGT
TGAAAGATACCATGGCAACATGACAGAAAATGAGTAAGACCATAGTTGAAAGACACCATGGCAAC
Found at i:9415904 original size:38 final size:38
Alignment explanation
Indices: 9415838--9415910 Score: 94
Period size: 38 Copynumber: 1.9 Consensus size: 38
9415828 ACCAATTTGG
* *
9415838 CACCCAGTGTCTTATCGGATAGTTCGAAGCAAAGTTGA
1 CACCCAGTGTCTCATCGGATAGTCCGAAGCAAAGTTGA
* *
9415876 CACCCAGTGTCTCATCGGCCTAG-CCGAAGTAAAGT
1 CACCCAGTGTCTCATCGG-ATAGTCCGAAGCAAAGT
9415911 GGTACCCAGT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
38 27 0.90
39 3 0.10
ACGTcount: A:0.27, C:0.26, G:0.23, T:0.23
Consensus pattern (38 bp):
CACCCAGTGTCTCATCGGATAGTCCGAAGCAAAGTTGA
Found at i:9417313 original size:16 final size:18
Alignment explanation
Indices: 9417281--9417315 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
9417271 TAATTAACCC
9417281 CTCAATTAAACTAATTTT
1 CTCAATTAAACTAATTTT
9417299 CTCAATT-AA-TAATTTT
1 CTCAATTAAACTAATTTT
9417315 C
1 C
9417316 CTAGACATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 2 0.12
18 7 0.41
ACGTcount: A:0.37, C:0.17, G:0.00, T:0.46
Consensus pattern (18 bp):
CTCAATTAAACTAATTTT
Found at i:9418096 original size:18 final size:18
Alignment explanation
Indices: 9418073--9418112 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
9418063 TTTTTGTACA
9418073 TTTCACAATTTCAAAATT
1 TTTCACAATTTCAAAATT
*
9418091 TTTCACTATTTCAAAATT
1 TTTCACAATTTCAAAATT
9418109 TTTC
1 TTTC
9418113 CTAACTTCAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.33, C:0.17, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTCACAATTTCAAAATT
Found at i:9418121 original size:18 final size:18
Alignment explanation
Indices: 9418082--9418121 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
9418072 ATTTCACAAT
*
9418082 TTCAAAATTTTTCACTAT
1 TTCAAAATTTTTCACTAC
9418100 TTCAAAATTTTTC-CTAAC
1 TTCAAAATTTTTCACT-AC
9418118 TTCA
1 TTCA
9418122 CATTTAACTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 2 0.10
18 18 0.90
ACGTcount: A:0.33, C:0.20, G:0.00, T:0.47
Consensus pattern (18 bp):
TTCAAAATTTTTCACTAC
Found at i:9421176 original size:2 final size:2
Alignment explanation
Indices: 9421171--9421195 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
9421161 AAAAAAAAAC
9421171 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
9421196 AAGTGGGGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:9421664 original size:30 final size:31
Alignment explanation
Indices: 9421623--9421694 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 31
9421613 ATATCTAAAC
* *
9421623 AATAACAACAAAATAGTGAAAAA-AATAAGA
1 AATAACAACAAAATAGTAAAAAATAACAAGA
*
9421653 AATAGCAACAAAATAGTAAAAAATAACAAGA
1 AATAACAACAAAATAGTAAAAAATAACAAGA
* *
9421684 AAAAAAAACAA
1 AATAACAACAA
9421695 CAAATTTTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
30 21 0.60
31 14 0.40
ACGTcount: A:0.72, C:0.08, G:0.08, T:0.11
Consensus pattern (31 bp):
AATAACAACAAAATAGTAAAAAATAACAAGA
Found at i:9422419 original size:33 final size:33
Alignment explanation
Indices: 9422381--9422489 Score: 87
Period size: 33 Copynumber: 3.2 Consensus size: 33
9422371 AGAAAAATCA
*
9422381 ATTATACATCATTCAATTTAATACTATTTTTAT
1 ATTATACATCATTTAATTTAATACTATTTTTAT
* * * ***
9422414 ATTATA-TTGATTTTAGGGTATTACAGGTTATTTTCT-T
1 ATTATACATCA-TTTA--AT-TTA-ATACTATTTT-TAT
9422451 ATTATACATCATTTAATTTAATACTATTTTTAT
1 ATTATACATCATTTAATTTAATACTATTTTTAT
9422484 ATTATA
1 ATTATA
9422490 TTGATTTTAG
Statistics
Matches: 55, Mismatches: 13, Indels: 16
0.65 0.15 0.19
Matches are distributed among these distances:
32 3 0.05
33 23 0.42
34 3 0.05
35 2 0.04
36 3 0.05
37 18 0.33
38 3 0.05
ACGTcount: A:0.33, C:0.08, G:0.06, T:0.53
Consensus pattern (33 bp):
ATTATACATCATTTAATTTAATACTATTTTTAT
Found at i:9422447 original size:37 final size:37
Alignment explanation
Indices: 9422405--9422526 Score: 114
Period size: 37 Copynumber: 3.4 Consensus size: 37
9422395 AATTTAATAC
*
9422405 TATTTTTATATTATATTGATTTTAGGGTATTACAGGT
1 TATTTTTATATTATATTGATTTTAGGGTATTACAGGA
* * * *
9422442 TATTTTCT-TATTATACATCA-TTTA--AT-TTA-A-TA
1 TATTTT-TATATTATA-TTGATTTTAGGGTATTACAGGA
9422474 CTATTTTTATATTATATTGATTTTAGGGTATTACAGGA
1 -TATTTTTATATTATATTGATTTTAGGGTATTACAGGA
*
9422512 TATTTTTTTATTATA
1 TATTTTTATATTATA
9422527 GTTTTTTTTT
Statistics
Matches: 65, Mismatches: 10, Indels: 20
0.68 0.11 0.21
Matches are distributed among these distances:
32 3 0.05
33 18 0.28
34 3 0.05
35 2 0.03
36 3 0.05
37 32 0.49
38 4 0.06
ACGTcount: A:0.30, C:0.05, G:0.10, T:0.56
Consensus pattern (37 bp):
TATTTTTATATTATATTGATTTTAGGGTATTACAGGA
Found at i:9422455 original size:70 final size:70
Alignment explanation
Indices: 9422381--9422526 Score: 265
Period size: 70 Copynumber: 2.1 Consensus size: 70
9422371 AGAAAAATCA
*
9422381 ATTATACATCATTCAATTTAATACTATTTTTATATTATATTGATTTTAGGGTATTACAGGTTATT
1 ATTATACATCATTCAATTTAATACTATTTTTATATTATATTGATTTTAGGGTATTACAGGATATT
9422446 TTCTT
66 TTCTT
*
9422451 ATTATACATCATTTAATTTAATACTATTTTTATATTATATTGATTTTAGGGTATTACAGGATATT
1 ATTATACATCATTCAATTTAATACTATTTTTATATTATATTGATTTTAGGGTATTACAGGATATT
*
9422516 TTTTT
66 TTCTT
9422521 ATTATA
1 ATTATA
9422527 GTTTTTTTTT
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
70 73 1.00
ACGTcount: A:0.32, C:0.07, G:0.08, T:0.53
Consensus pattern (70 bp):
ATTATACATCATTCAATTTAATACTATTTTTATATTATATTGATTTTAGGGTATTACAGGATATT
TTCTT
Found at i:9426409 original size:20 final size:21
Alignment explanation
Indices: 9426358--9426409 Score: 54
Period size: 19 Copynumber: 2.6 Consensus size: 21
9426348 GATAATTTTT
*
9426358 TAAAGTTAAATAATCAAAACG
1 TAAACTTAAATAATCAAAACG
* **
9426379 TGAACTT-AATAAT-AAATTG
1 TAAACTTAAATAATCAAAACG
9426398 TAAACTTAAATA
1 TAAACTTAAATA
9426410 TAATTTACTT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
19 10 0.40
20 10 0.40
21 5 0.20
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.31
Consensus pattern (21 bp):
TAAACTTAAATAATCAAAACG
Found at i:9443248 original size:25 final size:25
Alignment explanation
Indices: 9443214--9443264 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
9443204 CTTCAAGTAT
*
9443214 GTCATTTTCATAAAATCAGGAGCTA
1 GTCATTTTCATAAAATCAGGAACTA
9443239 GTCATTTTCATAAAATCAGGAACTA
1 GTCATTTTCATAAAATCAGGAACTA
9443264 G
1 G
9443265 ACTTCTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (25 bp):
GTCATTTTCATAAAATCAGGAACTA
Found at i:9449732 original size:10 final size:10
Alignment explanation
Indices: 9449703--9449735 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
9449693 ATTAGCAAAC
*
9449703 AAAAAAAAAA
1 AAAAAAAAAG
9449713 AAAAAAAAAG
1 AAAAAAAAAG
9449723 AAAAAAAAAG
1 AAAAAAAAAG
9449733 AAA
1 AAA
9449736 TGATAATTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.94, C:0.00, G:0.06, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:9459916 original size:9 final size:9
Alignment explanation
Indices: 9459902--9459927 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
9459892 ATCTGTGGAA
9459902 GCAGCAGCG
1 GCAGCAGCG
9459911 GCAGCAGCG
1 GCAGCAGCG
9459920 GCAGCAGC
1 GCAGCAGC
9459928 AATGCCATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.23, C:0.35, G:0.42, T:0.00
Consensus pattern (9 bp):
GCAGCAGCG
Found at i:9466466 original size:6 final size:6
Alignment explanation
Indices: 9466457--9466483 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
9466447 CAAAATTCGA
9466457 AAAAAC AAAAAC AAAAAC AAAAAC AAA
1 AAAAAC AAAAAC AAAAAC AAAAAC AAA
9466484 GAGATAATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAAAC
Found at i:9466800 original size:9 final size:8
Alignment explanation
Indices: 9466786--9466810 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
9466776 TTCTTTAAGC
9466786 AAAAAAAG
1 AAAAAAAG
9466794 AAAAAAAG
1 AAAAAAAG
9466802 AAAAAAAG
1 AAAAAAAG
9466810 A
1 A
9466811 GTTATTCGTA
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:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:9475898 original size:18 final size:16
Alignment explanation
Indices: 9475861--9475895 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
9475851 ATAGCTGTGG
*
9475861 AAATCTTAACGTACAA
1 AAATATTAACGTACAA
9475877 AAATATTAACGTACAA
1 AAATATTAACGTACAA
9475893 AAA
1 AAA
9475896 AATGTGGCCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.57, C:0.14, G:0.06, T:0.23
Consensus pattern (16 bp):
AAATATTAACGTACAA
Found at i:9482170 original size:29 final size:29
Alignment explanation
Indices: 9482115--9482170 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 29
9482105 AATCTACCCA
* * *
9482115 AAAATCTTGATTTTTAAGTTATCCTCACT
1 AAAATCTTGATCTTCAAGCTATCCTCACT
* *
9482144 AAAATCTTTATCTTCAAGCTATTCTCA
1 AAAATCTTGATCTTCAAGCTATCCTCA
9482171 AATGATTTTA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 22 1.00
ACGTcount: A:0.32, C:0.20, G:0.05, T:0.43
Consensus pattern (29 bp):
AAAATCTTGATCTTCAAGCTATCCTCACT
Found at i:9487776 original size:21 final size:22
Alignment explanation
Indices: 9487745--9487785 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
9487735 CTTACCATTT
9487745 TTAAAGTTAAAA-ATCAAAATCA
1 TTAAAGTTAAAACA-CAAAATCA
9487767 TTAAA-TTAAAACACAAAAT
1 TTAAAGTTAAAACACAAAAT
9487786 TACGTCATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.61, C:0.10, G:0.02, T:0.27
Consensus pattern (22 bp):
TTAAAGTTAAAACACAAAATCA
Found at i:9493022 original size:10 final size:11
Alignment explanation
Indices: 9493007--9493035 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
9492997 ACAATACATG
9493007 AAAACAGAG-C
1 AAAACAGAGCC
9493017 AAAACAGAGCC
1 AAAACAGAGCC
9493028 AAAACAGA
1 AAAACAGA
9493036 ATAAGGACAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.50
11 9 0.50
ACGTcount: A:0.62, C:0.21, G:0.17, T:0.00
Consensus pattern (11 bp):
AAAACAGAGCC
Found at i:9503543 original size:14 final size:15
Alignment explanation
Indices: 9503518--9503546 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
9503508 TATAATTTTA
9503518 ATATTTTAATAGTTT
1 ATATTTTAATAGTTT
9503533 ATATTTT-ATAGTTT
1 ATATTTTAATAGTTT
9503547 TTATAATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (15 bp):
ATATTTTAATAGTTT
Found at i:9503586 original size:29 final size:30
Alignment explanation
Indices: 9503535--9503601 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 30
9503525 AATAGTTTAT
* *
9503535 ATTTTATAGTTTTTATAATATTAAATTAAA
1 ATTTTATTGTTTTTATAAAATTAAATTAAA
* *
9503565 ATTTTATTTTTTTTA-AAAATTAAATTATA
1 ATTTTATTGTTTTTATAAAATTAAATTAAA
9503594 ATTTTATT
1 ATTTTATT
9503602 ATTATTAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
29 20 0.61
30 13 0.39
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (30 bp):
ATTTTATTGTTTTTATAAAATTAAATTAAA
Found at i:9503609 original size:29 final size:29
Alignment explanation
Indices: 9503554--9503609 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
9503544 TTTTTATAAT
* *
9503554 ATTAAATTAAAATTTTATTTTTTTTAAAA
1 ATTAAATTAAAATTTTATTATTATTAAAA
*
9503583 ATTAAATTATAATTTTATTATTATTAA
1 ATTAAATTAAAATTTTATTATTATTAA
9503610 TTTAAAATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (29 bp):
ATTAAATTAAAATTTTATTATTATTAAAA
Found at i:9505549 original size:20 final size:20
Alignment explanation
Indices: 9505524--9505571 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
9505514 CGTTTAATTA
*
9505524 ATTTTTAAAAACATTTTTAT-
1 ATTTTTAAAAA-ATTTTAATG
*
9505544 ATTTTTAAATAATTTTAATG
1 ATTTTTAAAAAATTTTAATG
9505564 ATTTTTAA
1 ATTTTTAA
9505572 TTTTTTTGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 7 0.28
20 18 0.72
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (20 bp):
ATTTTTAAAAAATTTTAATG
Found at i:9514601 original size:18 final size:17
Alignment explanation
Indices: 9514552--9514601 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
9514542 CCCATTTACT
9514552 TTCCCTCAAAC-TTT-TA
1 TTCCCT-AAACTTTTATA
*
9514568 TTCCCAAAACTTTTTATA
1 TTCCCTAAAC-TTTTATA
9514586 TTCCCCTAAACTTTTA
1 TT-CCCTAAACTTTTA
9514602 CTTCTCACCA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
15 4 0.14
16 5 0.18
17 3 0.11
18 9 0.32
19 7 0.25
ACGTcount: A:0.28, C:0.28, G:0.00, T:0.44
Consensus pattern (17 bp):
TTCCCTAAACTTTTATA
Found at i:9515285 original size:28 final size:28
Alignment explanation
Indices: 9515245--9515300 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
9515235 TCACCCCTAC
* *
9515245 CCTCAACATTTACAAAATTTGTCAATTT
1 CCTCAACATTTACAAAATCTATCAATTT
9515273 CCTCAACATTTACAAAATCTATCAATTT
1 CCTCAACATTTACAAAATCTATCAATTT
9515301 ACTCCTAGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.38, C:0.23, G:0.02, T:0.38
Consensus pattern (28 bp):
CCTCAACATTTACAAAATCTATCAATTT
Found at i:9520986 original size:22 final size:22
Alignment explanation
Indices: 9520936--9520979 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
9520926 ACAATATGAC
*
9520936 AATAAAATAATAGCAACATAAT
1 AATAAAATAATAGCAAAATAAT
* *
9520958 AATAAAATAGTAGTAAAATAAT
1 AATAAAATAATAGCAAAATAAT
9520980 GAAAAAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.64, C:0.05, G:0.07, T:0.25
Consensus pattern (22 bp):
AATAAAATAATAGCAAAATAAT
Found at i:9524720 original size:16 final size:15
Alignment explanation
Indices: 9524680--9524723 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 15
9524670 ATGTGATGAA
9524680 ATTGATATGAATATGTG
1 ATTGAT-TGAA-ATGTG
*
9524697 ATTAATTGAAATGTG
1 ATTGATTGAAATGTG
9524712 TATTGATTGAAA
1 -ATTGATTGAAA
9524724 ACTGGAAAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 5 0.21
16 14 0.58
17 5 0.21
ACGTcount: A:0.39, C:0.00, G:0.20, T:0.41
Consensus pattern (15 bp):
ATTGATTGAAATGTG
Found at i:9524814 original size:13 final size:13
Alignment explanation
Indices: 9524792--9524825 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
9524782 CATGCCATAG
*
9524792 GATTTTGAGAAGA
1 GATTTGGAGAAGA
*
9524805 GATTTGGAGATGA
1 GATTTGGAGAAGA
9524818 GATTTGGA
1 GATTTGGA
9524826 TATGCTGATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.35, T:0.32
Consensus pattern (13 bp):
GATTTGGAGAAGA
Found at i:9528023 original size:21 final size:21
Alignment explanation
Indices: 9527975--9528026 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
9527965 ATGTGTCATA
*
9527975 TTTCAGGCACCTTGTGTGTCG
1 TTTCAGGCACCTCGTGTGTCG
***
9527996 CAGCAGGCACCTCGTGTGTCG
1 TTTCAGGCACCTCGTGTGTCG
9528017 TTTCAGGCAC
1 TTTCAGGCAC
9528027 TTATGTGTCG
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.13, C:0.29, G:0.29, T:0.29
Consensus pattern (21 bp):
TTTCAGGCACCTCGTGTGTCG
Found at i:9529891 original size:28 final size:28
Alignment explanation
Indices: 9529831--9529893 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
9529821 ATGGCACGAA
** *
9529831 ATATTGAGAATGGCACTTAATGTGCGAG
1 ATATTGAGAATGAAACTTAATGTGCAAG
*
9529859 ATATTGAGAATGAAACTTAGTGTGCAA-
1 ATATTGAGAATGAAACTTAATGTGCAAG
9529886 AGTATTGA
1 A-TATTGA
9529894 ATGATTAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 1 0.03
28 29 0.97
ACGTcount: A:0.37, C:0.08, G:0.25, T:0.30
Consensus pattern (28 bp):
ATATTGAGAATGAAACTTAATGTGCAAG
Found at i:9530010 original size:39 final size:39
Alignment explanation
Indices: 9529966--9530149 Score: 314
Period size: 39 Copynumber: 4.7 Consensus size: 39
9529956 GACTTTATAA
*
9529966 TGGTGTTATATCCGGGCTAAGTCCCGAAGGCATTCGTGT
1 TGGTGTTATATCCGGGCTAAGTCCCGAAGGCATTCGTGC
* *
9530005 TGGTGTTATATCCGGGCTAAGTCCTGAAGGCATTCATGC
1 TGGTGTTATATCCGGGCTAAGTCCCGAAGGCATTCGTGC
9530044 TGGTGTTATATCCGGGCTAAGTCCCGAAGGCATTCGTGC
1 TGGTGTTATATCCGGGCTAAGTCCCGAAGGCATTCGTGC
*
9530083 TGGTGTTATATCCGGGCTAAGCCCCGAAGGCATTCGTGC
1 TGGTGTTATATCCGGGCTAAGTCCCGAAGGCATTCGTGC
9530122 TGGTGTTATATCCGGGCTTAAAGTCCCG
1 TGGTGTTATATCCGGGC-T-AAGTCCCG
9530150 CATGCTTTGT
Statistics
Matches: 136, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
39 128 0.94
40 1 0.01
41 7 0.05
ACGTcount: A:0.18, C:0.22, G:0.30, T:0.29
Consensus pattern (39 bp):
TGGTGTTATATCCGGGCTAAGTCCCGAAGGCATTCGTGC
Found at i:9532665 original size:37 final size:37
Alignment explanation
Indices: 9532615--9532689 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
9532605 AAAGAAAAAG
9532615 TTAACCTCCGCTAGTCGACTTATTCAGATACGATGTC
1 TTAACCTCCGCTAGTCGACTTATTCAGATACGATGTC
*
9532652 TTAACCTCGGCTAGTCGACTTATTCAGATACGATGTC
1 TTAACCTCCGCTAGTCGACTTATTCAGATACGATGTC
9532689 T
1 T
9532690 GAAGTATGTG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.33
Consensus pattern (37 bp):
TTAACCTCCGCTAGTCGACTTATTCAGATACGATGTC
Found at i:9546603 original size:18 final size:18
Alignment explanation
Indices: 9546580--9546615 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
9546570 TGGCTTCACC
9546580 TTAAATACAATCACAGCA
1 TTAAATACAATCACAGCA
9546598 TTAAATACAATCACAGCA
1 TTAAATACAATCACAGCA
9546616 GAGTAATTCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.22, G:0.06, T:0.22
Consensus pattern (18 bp):
TTAAATACAATCACAGCA
Found at i:9546748 original size:24 final size:24
Alignment explanation
Indices: 9546720--9546767 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
9546710 TTGTTATCAG
9546720 TAAGATGTTAAATTAAGTAAAAAT
1 TAAGATGTTAAATTAAGTAAAAAT
9546744 TAAGATGTTAAATTAAGTAAAAAT
1 TAAGATGTTAAATTAAGTAAAAAT
9546768 GGTGTACCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.00, G:0.12, T:0.33
Consensus pattern (24 bp):
TAAGATGTTAAATTAAGTAAAAAT
Found at i:9546758 original size:13 final size:13
Alignment explanation
Indices: 9546720--9546760 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
9546710 TTGTTATCAG
9546720 TAAGATGTTAAAT
1 TAAGATGTTAAAT
**
9546733 TAAG-T-AAAAAT
1 TAAGATGTTAAAT
9546744 TAAGATGTTAAAT
1 TAAGATGTTAAAT
9546757 TAAG
1 TAAG
9546761 TAAAAATGGT
Statistics
Matches: 22, Mismatches: 4, Indels: 4
0.73 0.13 0.13
Matches are distributed among these distances:
11 8 0.36
12 2 0.09
13 12 0.55
ACGTcount: A:0.51, C:0.00, G:0.15, T:0.34
Consensus pattern (13 bp):
TAAGATGTTAAAT
Found at i:9549579 original size:16 final size:16
Alignment explanation
Indices: 9549558--9549598 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
9549548 TAATGCCAAA
9549558 ATAAAATTAT-TAAGAT
1 ATAAAATTATATAA-AT
9549574 ATAAAATTCATATAAAT
1 ATAAAATT-ATATAAAT
9549591 -TAAAATTA
1 ATAAAATTA
9549599 CTTTTAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 1 0.04
16 15 0.65
17 4 0.17
18 3 0.13
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (16 bp):
ATAAAATTATATAAAT
Found at i:9557737 original size:19 final size:18
Alignment explanation
Indices: 9557704--9557739 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
9557694 CTTTTTACCA
9557704 TTTTTTATAATTTTATAT
1 TTTTTTATAATTTTATAT
*
9557722 TTTTTTATGATATTTATA
1 TTTTTTATAAT-TTTATA
9557740 ATATTTTGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (18 bp):
TTTTTTATAATTTTATAT
Found at i:9559336 original size:10 final size:10
Alignment explanation
Indices: 9559323--9559352 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
9559313 ATAATATTCT
9559323 ATAATTTTTA
1 ATAATTTTTA
9559333 ATAATTTTTA
1 ATAATTTTTA
9559343 ATAATTTTTA
1 ATAATTTTTA
9559353 TATTCTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (10 bp):
ATAATTTTTA
Found at i:9559336 original size:20 final size:20
Alignment explanation
Indices: 9559286--9559352 Score: 61
Period size: 20 Copynumber: 3.4 Consensus size: 20
9559276 AATTCTTTTG
*
9559286 AATTTTTAAATAA-TTCCAAT
1 AATTTTT-AATAATTTCTAAT
9559306 -ATCTTTT-ATAATATTCT-AT
1 AAT-TTTTAATAAT-TTCTAAT
*
9559325 AATTTTTAATAATTTTTAAT
1 AATTTTTAATAATTTCTAAT
9559345 AATTTTTA
1 AATTTTTA
9559353 TATTCTTTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
18 4 0.10
19 11 0.28
20 24 0.62
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (20 bp):
AATTTTTAATAATTTCTAAT
Found at i:9560105 original size:24 final size:24
Alignment explanation
Indices: 9560054--9560105 Score: 79
Period size: 23 Copynumber: 2.2 Consensus size: 24
9560044 AGATTTAGAA
*
9560054 TTTTTGTTTACTCTTGTAGCACGG
1 TTTTTGTCTACTCTTGTAGCACGG
*
9560078 TTTTTGTCTAC-CTTGTAGCACGT
1 TTTTTGTCTACTCTTGTAGCACGG
9560101 TTTTT
1 TTTTT
9560106 AGTTTGCTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 16 0.62
24 10 0.38
ACGTcount: A:0.12, C:0.17, G:0.17, T:0.54
Consensus pattern (24 bp):
TTTTTGTCTACTCTTGTAGCACGG
Found at i:9562230 original size:90 final size:90
Alignment explanation
Indices: 9561614--9562218 Score: 933
Period size: 90 Copynumber: 6.7 Consensus size: 90
9561604 GTGGACCCAT
* * * *
9561614 GGTTTGCGCATTGACTAGAGCAGGAGAAACAGTTTGCAT-GCTAGTAGCTGAGCCAGTTGAAGGG
1 GGTTTGTGCATTGACTACAGCAGGTGAAACAGTTTGCATAG-TAGAAGCTGAGCCAGTTGAAGGG
* *
9561678 ATCCCTGAAGCAGTGGAAGGCTGCAA
65 ATCCCTGAAGCAGTAGAACGCTGCAA
* *
9561704 GGTTTGTGCATTGACTACAGCAGGTGAAACAGTTTGCATACTAGAAGCTGAGCCAGTTGGAGGGA
1 GGTTTGTGCATTGACTACAGCAGGTGAAACAGTTTGCATAGTAGAAGCTGAGCCAGTTGAAGGGA
* *
9561769 TCCCTGAAGCAGTGGAAGGCTGCAA
66 TCCCTGAAGCAGTAGAACGCTGCAA
* * * * * *
9561794 GGTTTGTGCATTGGCTGCAGCAAGTGAAACAGTTTGCACAGTAGAAGTTGAGCTAGTTGAAGGGA
1 GGTTTGTGCATTGACTACAGCAGGTGAAACAGTTTGCATAGTAGAAGCTGAGCCAGTTGAAGGGA
*
9561859 TCCCTGAAGTAGTAGAACGCTGCAA
66 TCCCTGAAGCAGTAGAACGCTGCAA
* * *
9561884 AGTTTGTGCATTGACTACAACAGGTGAAACAGTTTGCACAGTAGAAGCTGAGCCAGTTGAAGGGA
1 GGTTTGTGCATTGACTACAGCAGGTGAAACAGTTTGCATAGTAGAAGCTGAGCCAGTTGAAGGGA
*
9561949 TCCCTGAAGTAGTAGAACGCTGCAA
66 TCCCTGAAGCAGTAGAACGCTGCAA
* *
9561974 GGTTTGTGCATTGACTACAGCAGGTGAAACAGTTTGCATGGTAGAAGCTGAGCCAGTTGAAGGAA
1 GGTTTGTGCATTGACTACAGCAGGTGAAACAGTTTGCATAGTAGAAGCTGAGCCAGTTGAAGGGA
9562039 TCCCTGAAGCAGTAGAACGCTGCAA
66 TCCCTGAAGCAGTAGAACGCTGCAA
*
9562064 TGTTTGTGCATTGACTACAGCAGGTGAAACAGTTTGCATAGTAGAAGCTGAGCCAGTTGAAGGGA
1 GGTTTGTGCATTGACTACAGCAGGTGAAACAGTTTGCATAGTAGAAGCTGAGCCAGTTGAAGGGA
9562129 TCCCTGAAGCAGTAGAACGCTGCAA
66 TCCCTGAAGCAGTAGAACGCTGCAA
** * * *
9562154 TATTTGTGCATTAACTACAGCAGGTGAAACAGTTCGCATACTAGAAGCTGAGCCAGTTGAAGGGA
1 GGTTTGTGCATTGACTACAGCAGGTGAAACAGTTTGCATAGTAGAAGCTGAGCCAGTTGAAGGGA
9562219 GACCAGAAGC
Statistics
Matches: 477, Mismatches: 37, Indels: 2
0.92 0.07 0.00
Matches are distributed among these distances:
90 477 1.00
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (90 bp):
GGTTTGTGCATTGACTACAGCAGGTGAAACAGTTTGCATAGTAGAAGCTGAGCCAGTTGAAGGGA
TCCCTGAAGCAGTAGAACGCTGCAA
Found at i:9563568 original size:47 final size:47
Alignment explanation
Indices: 9563499--9563591 Score: 186
Period size: 47 Copynumber: 2.0 Consensus size: 47
9563489 GTATTGAAAG
9563499 TATAATCTCTCCAAATCTCAAAATAGTCTCCTTACCACAAGTATAGA
1 TATAATCTCTCCAAATCTCAAAATAGTCTCCTTACCACAAGTATAGA
9563546 TATAATCTCTCCAAATCTCAAAATAGTCTCCTTACCACAAGTATAG
1 TATAATCTCTCCAAATCTCAAAATAGTCTCCTTACCACAAGTATAG
9563592 GTTAAATAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.38, C:0.26, G:0.06, T:0.30
Consensus pattern (47 bp):
TATAATCTCTCCAAATCTCAAAATAGTCTCCTTACCACAAGTATAGA
Found at i:9570082 original size:123 final size:123
Alignment explanation
Indices: 9569863--9570109 Score: 494
Period size: 123 Copynumber: 2.0 Consensus size: 123
9569853 AATTTGACAG
9569863 TATGATAAAAGACAAACCAAGTAGTATTTTATGCTTTTGGACATCCAAAATAAATAAAATAATTT
1 TATGATAAAAGACAAACCAAGTAGTATTTTATGCTTTTGGACATCCAAAATAAATAAAATAATTT
9569928 CAAACAACAGAATTCAAGTGGTAAGACTGGGATGAGTATTGGGTAAAGATCCTAGGTT
66 CAAACAACAGAATTCAAGTGGTAAGACTGGGATGAGTATTGGGTAAAGATCCTAGGTT
9569986 TATGATAAAAGACAAACCAAGTAGTATTTTATGCTTTTGGACATCCAAAATAAATAAAATAATTT
1 TATGATAAAAGACAAACCAAGTAGTATTTTATGCTTTTGGACATCCAAAATAAATAAAATAATTT
9570051 CAAACAACAGAATTCAAGTGGTAAGACTGGGATGAGTATTGGGTAAAGATCCTAGGTT
66 CAAACAACAGAATTCAAGTGGTAAGACTGGGATGAGTATTGGGTAAAGATCCTAGGTT
9570109 T
1 T
9570110 TAGCTGTCAC
Statistics
Matches: 124, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
123 124 1.00
ACGTcount: A:0.41, C:0.11, G:0.19, T:0.29
Consensus pattern (123 bp):
TATGATAAAAGACAAACCAAGTAGTATTTTATGCTTTTGGACATCCAAAATAAATAAAATAATTT
CAAACAACAGAATTCAAGTGGTAAGACTGGGATGAGTATTGGGTAAAGATCCTAGGTT
Found at i:9578197 original size:42 final size:42
Alignment explanation
Indices: 9577949--9578189 Score: 358
Period size: 42 Copynumber: 5.7 Consensus size: 42
9577939 TTAAATCATT
*
9577949 ATCTCCATCATCCTTAGCTTTCCTACTAGAAGATCTAGTACC
1 ATCTCCATCATCCTTAGCTTTCCTACTAGACGATCTAGTACC
* * *
9577991 ATCTCCATCATCCTTAGCCTTCCTACTAGATGATCTGGTACC
1 ATCTCCATCATCCTTAGCTTTCCTACTAGACGATCTAGTACC
* * *
9578033 ATCTCCATCATTCTTAGCTTTCCTACTAGAGGATCTGGTACC
1 ATCTCCATCATCCTTAGCTTTCCTACTAGACGATCTAGTACC
* * * *
9578075 ACCTCCATCATCCTCAGCTTTCCTACTAGGCGATCTAATACC
1 ATCTCCATCATCCTTAGCTTTCCTACTAGACGATCTAGTACC
*
9578117 ATCTCCGTCATCCTTAGCTTTCCTA-TCAGACGATCTAGTACC
1 ATCTCCATCATCCTTAGCTTTCCTACT-AGACGATCTAGTACC
9578159 ATCTCCATCATCCTTAGCTTTCCTACTAGAC
1 ATCTCCATCATCCTTAGCTTTCCTACTAGAC
9578190 AACCTAGTGC
Statistics
Matches: 178, Mismatches: 19, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
41 1 0.01
42 176 0.99
43 1 0.01
ACGTcount: A:0.23, C:0.33, G:0.11, T:0.33
Consensus pattern (42 bp):
ATCTCCATCATCCTTAGCTTTCCTACTAGACGATCTAGTACC
Found at i:9579134 original size:24 final size:24
Alignment explanation
Indices: 9579090--9579135 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
9579080 CTATTTTATT
* *
9579090 ATTTATTTTTATTAATATTAAATA
1 ATTTATTTTAATAAATATTAAATA
*
9579114 ATTTATTTTAATAAATTTTAAA
1 ATTTATTTTAATAAATATTAAA
9579136 AATAATATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
ATTTATTTTAATAAATATTAAATA
Found at i:9581254 original size:13 final size:15
Alignment explanation
Indices: 9581236--9581267 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
9581226 AAATATCATG
9581236 TATTTTTTA-TA-TA
1 TATTTTTTAGTATTA
9581249 TATTTTTTAGTATTA
1 TATTTTTTAGTATTA
9581264 TATT
1 TATT
9581268 ATATTTTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 9 0.53
14 2 0.12
15 6 0.35
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (15 bp):
TATTTTTTAGTATTA
Found at i:9581734 original size:24 final size:24
Alignment explanation
Indices: 9581707--9581778 Score: 73
Period size: 24 Copynumber: 3.2 Consensus size: 24
9581697 ATTTAATTTG
9581707 ATTAAGGTTTATTGGGTTTTAGTT
1 ATTAAGGTTTATTGGGTTTTAGTT
* * * *
9581731 ATTAAAG-TGATT-TGATTT-G--
1 ATTAAGGTTTATTGGGTTTTAGTT
9581750 ATTAAGGTTTATTGGGTTTTAGTT
1 ATTAAGGTTTATTGGGTTTTAGTT
9581774 ATTAA
1 ATTAA
9581779 ATAAAGTATA
Statistics
Matches: 35, Mismatches: 8, Indels: 10
0.66 0.15 0.19
Matches are distributed among these distances:
19 6 0.17
20 4 0.11
21 5 0.14
22 5 0.14
23 4 0.11
24 11 0.31
ACGTcount: A:0.26, C:0.00, G:0.22, T:0.51
Consensus pattern (24 bp):
ATTAAGGTTTATTGGGTTTTAGTT
Found at i:9581749 original size:43 final size:43
Alignment explanation
Indices: 9581687--9581779 Score: 168
Period size: 43 Copynumber: 2.1 Consensus size: 43
9581677 ATTAACCTAA
9581687 ATTAAGAGTGATTTAATTTGATTAAGGTTTATTGGGTTTTAGTT
1 ATTAA-AGTGATTTAATTTGATTAAGGTTTATTGGGTTTTAGTT
*
9581731 ATTAAAGTGATTTGATTTGATTAAGGTTTATTGGGTTTTAGTT
1 ATTAAAGTGATTTAATTTGATTAAGGTTTATTGGGTTTTAGTT
9581774 ATTAAA
1 ATTAAA
9581780 TAAAGTATAT
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
43 43 0.90
44 5 0.10
ACGTcount: A:0.29, C:0.00, G:0.22, T:0.49
Consensus pattern (43 bp):
ATTAAAGTGATTTAATTTGATTAAGGTTTATTGGGTTTTAGTT
Found at i:9582982 original size:13 final size:15
Alignment explanation
Indices: 9582952--9582983 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
9582942 TCATTTCATG
9582952 CATTTCATCAATAAT
1 CATTTCATCAATAAT
9582967 CATTTCAT-AA-AAT
1 CATTTCATCAATAAT
9582980 CATT
1 CATT
9582984 ATTTCATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 2 0.12
15 8 0.47
ACGTcount: A:0.41, C:0.19, G:0.00, T:0.41
Consensus pattern (15 bp):
CATTTCATCAATAAT
Found at i:9584565 original size:46 final size:44
Alignment explanation
Indices: 9584460--9584567 Score: 135
Period size: 44 Copynumber: 2.4 Consensus size: 44
9584450 TGTCTTTGAC
** * * *
9584460 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
9584504 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
*
9584550 ATGGGCTTACATGGCTCA
1 ATGGACTTACATGGCTCA
9584568 TTTCTGTTCT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 33 0.60
46 22 0.40
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:9587109 original size:3 final size:3
Alignment explanation
Indices: 9587101--9587142 Score: 50
Period size: 3 Copynumber: 13.3 Consensus size: 3
9587091 ATATAAAAAT
9587101 ATA ATA ATA AT- ATA ATA TATA ATA TATA ATA ATA CATA ATA A
1 ATA ATA ATA ATA ATA ATA -ATA ATA -ATA ATA ATA -ATA ATA A
9587143 ACATATTTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
2 2 0.06
3 24 0.69
4 9 0.26
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:9587122 original size:7 final size:7
Alignment explanation
Indices: 9587098--9587173 Score: 55
Period size: 7 Copynumber: 10.1 Consensus size: 7
9587088 TATATATAAA
9587098 AATATAAT
1 AATAT-AT
9587106 AATAATAT
1 AAT-ATAT
9587114 AATATAT
1 AATATAT
9587121 AATATAT
1 AATATAT
9587128 AATA-AT
1 AATATAT
*
9587134 ACATAATAA
1 A-AT-ATAT
*
9587143 ACATATTT
1 A-ATATAT
* *
9587151 ATTATTT
1 AATATAT
9587158 AATAATAT
1 AAT-ATAT
9587166 AATATAT
1 AATATAT
9587173 A
1 A
9587174 TTAAATTTAA
Statistics
Matches: 57, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
6 3 0.05
7 29 0.51
8 18 0.32
9 7 0.12
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (7 bp):
AATATAT
Found at i:9587134 original size:10 final size:10
Alignment explanation
Indices: 9587089--9587142 Score: 63
Period size: 10 Copynumber: 5.1 Consensus size: 10
9587079 ACTTTACTAT
*
9587089 ATATATAAAA
1 ATATATAATA
9587099 ATATAATAATA
1 ATAT-ATAATA
9587110 ATATAATATATA
1 ATAT-ATA-ATA
9587122 ATATATAATA
1 ATATATAATA
*
9587132 ATACATAATA
1 ATATATAATA
9587142 A
1 A
9587143 ACATATTTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
10 17 0.43
11 16 0.40
12 7 0.17
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (10 bp):
ATATATAATA
Found at i:9587585 original size:14 final size:14
Alignment explanation
Indices: 9587561--9587597 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
9587551 CACGATTTTA
*
9587561 ATTTATTTAATAAT
1 ATTTATATAATAAT
*
9587575 ATTTTTATAATAAT
1 ATTTATATAATAAT
9587589 ATTTATATA
1 ATTTATATA
9587598 TCTAAGAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
ATTTATATAATAAT
Found at i:9595788 original size:16 final size:16
Alignment explanation
Indices: 9595752--9595791 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
9595742 TTATTTTGTT
*
9595752 CAATTTAAATTTATTA
1 CAATATAAATTTATTA
*
9595768 CAATATAAATTTTTTA
1 CAATATAAATTTATTA
*
9595784 GAATATAA
1 CAATATAA
9595792 TGTTAATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (16 bp):
CAATATAAATTTATTA
Found at i:9598611 original size:2 final size:2
Alignment explanation
Indices: 9598604--9598633 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
9598594 TCAATATAAC
9598604 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
9598634 AAGGATGGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:9609346 original size:13 final size:14
Alignment explanation
Indices: 9609330--9609365 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
9609320 CAATCTCATA
9609330 TCTCAATTTCAA-T
1 TCTCAATTTCAATT
9609343 TCTCAA-TTCAATT
1 TCTCAATTTCAATT
9609356 TCTC-ATTTCA
1 TCTCAATTTCA
9609366 TTCCAATAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (14 bp):
TCTCAATTTCAATT
Found at i:9609355 original size:18 final size:19
Alignment explanation
Indices: 9609317--9609357 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
9609307 TGGTTCATGT
9609317 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
9609336 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
9609354 TTTC
1 TTTC
9609358 TCATTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:9609547 original size:39 final size:38
Alignment explanation
Indices: 9609480--9609614 Score: 101
Period size: 39 Copynumber: 3.4 Consensus size: 38
9609470 ACCAATATGG
* * *
9609480 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATATTTGA
1 CACCCAGTGCCTCATCGGCTAG-CCGAAGAAATATTTGA
* * * *
9609519 CACCCAGTGTCTCATCGGCCTAGCCGAAGTAA-AGTTGG
1 CACCCAGTGCCTCATCGG-CTAGCCGAAGAAATATTTGA
* * * * *
9609557 TACCCAGTACCTCATCGAATCTATCCGAAGAAATATAGTGA
1 CACCCAGTGCCTCATCG--GCTAGCCGAAGAAATAT-TTGA
*
9609598 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
9609615 ACTCGAGGTC
Statistics
Matches: 73, Mismatches: 18, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
38 18 0.25
39 35 0.48
40 4 0.05
41 16 0.22
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (38 bp):
CACCCAGTGCCTCATCGGCTAGCCGAAGAAATATTTGA
Found at i:9609880 original size:18 final size:19
Alignment explanation
Indices: 9609854--9609892 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
9609844 TTTCAATTCA
9609854 ATTCAAATAATCAATATAT
1 ATTCAAATAATCAATATAT
*
9609873 ATTC-AATATTCAATATAT
1 ATTCAAATAATCAATATAT
9609891 AT
1 AT
9609893 ATCTATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTCAAATAATCAATATAT
Found at i:9611219 original size:5 final size:5
Alignment explanation
Indices: 9611209--9611261 Score: 61
Period size: 5 Copynumber: 10.0 Consensus size: 5
9611199 TTACTTATTT
* *
9611209 ATATA ATATAA TATATA ATATA ATATA CTATA ATATA ATAATA ATTTA
1 ATATA ATAT-A -ATATA ATATA ATATA ATATA ATATA AT-ATA ATATA
9611257 ATATA
1 ATATA
9611262 TATTTTAACA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
5 30 0.73
6 7 0.17
7 4 0.10
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (5 bp):
ATATA
Found at i:9611225 original size:12 final size:12
Alignment explanation
Indices: 9611208--9611263 Score: 69
Period size: 12 Copynumber: 4.5 Consensus size: 12
9611198 TTTACTTATT
9611208 TATATAATATAA
1 TATATAATATAA
9611220 TATATAATATAATA
1 TATATAATAT-A-A
9611234 TACTATAATATAA
1 TA-TATAATATAA
*
9611247 TA-ATAATTTAA
1 TATATAATATAA
9611258 TATATA
1 TATATA
9611264 TTTTAACACA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
11 10 0.26
12 13 0.33
13 4 0.10
14 4 0.10
15 8 0.21
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (12 bp):
TATATAATATAA
Found at i:9615790 original size:13 final size:14
Alignment explanation
Indices: 9615774--9615809 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
9615764 CAATCTCATA
9615774 TCTCAATTTCAA-T
1 TCTCAATTTCAATT
9615787 TCTCAA-TTCAATT
1 TCTCAATTTCAATT
9615800 TCTC-ATTTCA
1 TCTCAATTTCA
9615810 TTCCAATAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (14 bp):
TCTCAATTTCAATT
Found at i:9615799 original size:18 final size:19
Alignment explanation
Indices: 9615761--9615801 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
9615751 TGGTTCATGT
9615761 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
9615780 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
9615798 TTTC
1 TTTC
9615802 TCATTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:9615991 original size:39 final size:38
Alignment explanation
Indices: 9615924--9616058 Score: 101
Period size: 39 Copynumber: 3.4 Consensus size: 38
9615914 ACCAATATGG
* * *
9615924 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATATTTGA
1 CACCCAGTGCCTCATCGGCTAG-CCGAAGAAATATTTGA
* * * *
9615963 CACCCAGTGTCTCATCGGCCTAGCCGAAGTAA-AGTTGG
1 CACCCAGTGCCTCATCGG-CTAGCCGAAGAAATATTTGA
* * * * *
9616001 TACCCAGTACCTCATCGAATCTATCCGAAGAAATATAGTGA
1 CACCCAGTGCCTCATCG--GCTAGCCGAAGAAATAT-TTGA
*
9616042 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
9616059 ACTCGAGGTC
Statistics
Matches: 73, Mismatches: 18, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
38 18 0.25
39 35 0.48
40 4 0.05
41 16 0.22
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (38 bp):
CACCCAGTGCCTCATCGGCTAGCCGAAGAAATATTTGA
Found at i:9616324 original size:18 final size:19
Alignment explanation
Indices: 9616298--9616336 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
9616288 TTTCAATTCA
9616298 ATTCAAATAATCAATATAT
1 ATTCAAATAATCAATATAT
*
9616317 ATTC-AATATTCAATATAT
1 ATTCAAATAATCAATATAT
9616335 AT
1 AT
9616337 ATCTATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTCAAATAATCAATATAT
Found at i:9617664 original size:5 final size:5
Alignment explanation
Indices: 9617654--9617705 Score: 52
Period size: 5 Copynumber: 10.0 Consensus size: 5
9617644 TTACTTATTT
* *
9617654 ATATA ATATA ATAT- ATAATA TATATA CTATA ATATA ATAATA ATTTA
1 ATATA ATATA ATATA AT-ATA -ATATA ATATA ATATA AT-ATA ATATA
9617701 ATATA
1 ATATA
9617706 TATTTTAACA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
4 2 0.05
5 27 0.69
6 8 0.21
7 2 0.05
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (5 bp):
ATATA
Found at i:9617679 original size:21 final size:22
Alignment explanation
Indices: 9617653--9617705 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
9617643 TTTACTTATT
9617653 TATATAATATAATAT-ATAATA
1 TATATAATATAATATAATAATA
*
9617674 TATATACTATAATATAATAATA
1 TATATAATATAATATAATAATA
*
9617696 -ATTTAATATA
1 TATATAATATA
9617706 TATTTTAACA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 22 0.79
22 6 0.21
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
TATATAATATAATATAATAATA
Found at i:9617702 original size:16 final size:15
Alignment explanation
Indices: 9617650--9617705 Score: 53
Period size: 16 Copynumber: 3.7 Consensus size: 15
9617640 TTCTTTACTT
9617650 ATTT-ATATAATATA
1 ATTTAATATAATATA
9617664 ATATATAATAT-ATATA
1 AT-T-TAATATAATATA
* *
9617680 CTATAATATAATAATA
1 ATTTAATATAAT-ATA
9617696 ATTTAATATA
1 ATTTAATATA
9617706 TATTTTAACA
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 8 0.24
15 3 0.09
16 18 0.55
17 4 0.12
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.45
Consensus pattern (15 bp):
ATTTAATATAATATA
Found at i:9635619 original size:30 final size:30
Alignment explanation
Indices: 9635565--9635621 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
9635555 TTTACGAGCA
*
9635565 TTGGGGCAAAAGTGCAAATATGTAAAAGTT
1 TTGGGGCAAAAGTGAAAATATGTAAAAGTT
*
9635595 TTGGGGTCAAAA-TGAAAATTTGTAAAA
1 TTGGGG-CAAAAGTGAAAATATGTAAAA
9635622 ATATGATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 19 0.79
31 5 0.21
ACGTcount: A:0.42, C:0.05, G:0.25, T:0.28
Consensus pattern (30 bp):
TTGGGGCAAAAGTGAAAATATGTAAAAGTT
Found at i:9649352 original size:2 final size:2
Alignment explanation
Indices: 9649347--9649371 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
9649337 CTATGGGGGG
9649347 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
9649372 CTTGGATGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:9659155 original size:93 final size:93
Alignment explanation
Indices: 9659023--9659193 Score: 252
Period size: 93 Copynumber: 1.8 Consensus size: 93
9659013 GCCCATAAGT
** * *
9659023 GAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTAAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGAACATTCACATCCATAAGTGAACTCGGACTAAACTCAA
9659088 CGAGCTCGGATGCCTAGTTACATCTCAC
66 CGAGCTCGGATGCCTAGTTACATCTCAC
* * * * *
9659116 GAACTCGGACTCAACTCAGCGAGTTCGAACATTCACATCCATAAGTGAACTCGGATTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGAACATTCACATCCATAAGTGAACTCGGACTAAACTCAA
*
9659181 CGAGTTCGGATGC
66 CGAGCTCGGATGC
9659194 TCAACCATCC
Statistics
Matches: 68, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
93 68 1.00
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.21
Consensus pattern (93 bp):
GAACTCAGACTCAACTCAACGAGCTCGAACATTCACATCCATAAGTGAACTCGGACTAAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCAC
Found at i:9659209 original size:46 final size:46
Alignment explanation
Indices: 9659015--9659188 Score: 138
Period size: 46 Copynumber: 3.8 Consensus size: 46
9659005 TGTAACCCGC
* * ** ** *
9659015 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGAACACTCACAT
* * * * *
9659061 CCATAAGTGAACTCGGACTAAACTCAACGAGCTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTC-GA--AC-ACTCACAT
* * * *
9659111 -C-TCA-CGAACTCGGACTCAACTCAGCGAGTTCGAACATTCACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGAACACTCACAT
*
9659154 CCATAAGTGAACTCGGATTCAACTCAACGAGTTCG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCG
9659189 GATGCTCAAC
Statistics
Matches: 101, Mismatches: 20, Indels: 14
0.75 0.15 0.10
Matches are distributed among these distances:
43 6 0.06
44 2 0.02
45 2 0.02
46 59 0.58
47 24 0.24
48 2 0.02
49 2 0.02
50 4 0.04
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGAACACTCACAT
Done.