Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015046.1 Kokia drynarioides strain JFW-HI SEQ_130090, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 327920
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 261 characters in sequence are not A, C, G, or T
Found at i:17247 original size:18 final size:18
Alignment explanation
Indices: 17224--17262 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
17214 GTGATCTAAG
17224 TTTATATAT-TTTTGAAAA
1 TTTATATATATTTT-AAAA
17242 TTTATATATATTTTAAAA
1 TTTATATATATTTTAAAA
17260 TTT
1 TTT
17263 TTAAGTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (18 bp):
TTTATATATATTTTAAAA
Found at i:17251 original size:20 final size:19
Alignment explanation
Indices: 17226--17292 Score: 66
Period size: 20 Copynumber: 3.5 Consensus size: 19
17216 GATCTAAGTT
17226 TATATATTTTTGAAAATTTA
1 TATATATTTTT-AAAATTTA
*
17246 TATATA-TTTTAAAATTTT
1 TATATATTTTTAAAATTTA
* *
17264 TA-AGTTTTTTTATAAATTTC
1 TATA-TATTTTTA-AAATTTA
17284 TATATATTT
1 TATATATTT
17293 ATTTTTTTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
17 1 0.03
18 10 0.26
19 9 0.23
20 18 0.46
21 1 0.03
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.60
Consensus pattern (19 bp):
TATATATTTTTAAAATTTA
Found at i:23567 original size:38 final size:39
Alignment explanation
Indices: 23510--23589 Score: 144
Period size: 38 Copynumber: 2.1 Consensus size: 39
23500 CATATTATAT
23510 AATCACTTACAATGATTAGTTGGGATAAATTTGCATTTG
1 AATCACTTACAATGATTAGTTGGGATAAATTTGCATTTG
*
23549 AATCACTTA-GATGATTAGTTGGGATAAATTTGCATTTG
1 AATCACTTACAATGATTAGTTGGGATAAATTTGCATTTG
23587 AAT
1 AAT
23590 TTGAAGCCAT
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
38 31 0.77
39 9 0.22
ACGTcount: A:0.34, C:0.09, G:0.19, T:0.39
Consensus pattern (39 bp):
AATCACTTACAATGATTAGTTGGGATAAATTTGCATTTG
Found at i:28104 original size:34 final size:34
Alignment explanation
Indices: 28061--28129 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
28051 TTTTCCCTTA
28061 AGCATTTGGACTAATATTTTCCATATATAACTTT
1 AGCATTTGGACTAATATTTTCCATATATAACTTT
28095 AGCATTTGGACTAATATTTTCCATATATAACTTT
1 AGCATTTGGACTAATATTTTCCATATATAACTTT
28129 A
1 A
28130 TTAATGATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.33, C:0.14, G:0.09, T:0.43
Consensus pattern (34 bp):
AGCATTTGGACTAATATTTTCCATATATAACTTT
Found at i:28172 original size:43 final size:43
Alignment explanation
Indices: 28107--28194 Score: 167
Period size: 43 Copynumber: 2.0 Consensus size: 43
28097 CATTTGGACT
28107 AATATTTTCCATATATAACTTTATTAATGATATTTACAAATTA
1 AATATTTTCCATATATAACTTTATTAATGATATTTACAAATTA
*
28150 AATATTTTCCATATATACCTTTATTAATGATATTTACAAATTA
1 AATATTTTCCATATATAACTTTATTAATGATATTTACAAATTA
28193 AA
1 AA
28195 CTTTTTTTAA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.42, C:0.10, G:0.02, T:0.45
Consensus pattern (43 bp):
AATATTTTCCATATATAACTTTATTAATGATATTTACAAATTA
Found at i:31348 original size:2 final size:2
Alignment explanation
Indices: 31343--31368 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
31333 ATTATATATA
31343 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
31369 AACTTTTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:34353 original size:3 final size:3
Alignment explanation
Indices: 34345--34376 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
34335 GAACATTCAC
34345 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
34377 GAATCACCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:43296 original size:58 final size:59
Alignment explanation
Indices: 43219--43347 Score: 140
Period size: 58 Copynumber: 2.2 Consensus size: 59
43209 ACAGTTTTTT
* *
43219 AATTTGGTACCT-AATCTTGACACATCTTT-TTAAGTTGGTA-CTTAATCTTTTTGGGTTC
1 AATTTGGTACTTGAATCTTGAC-CATCTTTCTTAAGTTGGTATC-TAATATTTTTGGGTTC
* * * **
43277 AATTTGGTACTTGAA-CTTGACTATTTTTCTTAATTTGGTATCTAATATTTTTTTGTTC
1 AATTTGGTACTTGAATCTTGACCATCTTTCTTAAGTTGGTATCTAATATTTTTGGGTTC
*
43335 GATTTGGTACTTG
1 AATTTGGTACTTG
43348 TTAAATGTTT
Statistics
Matches: 60, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
57 5 0.08
58 52 0.87
59 3 0.05
ACGTcount: A:0.22, C:0.12, G:0.16, T:0.50
Consensus pattern (59 bp):
AATTTGGTACTTGAATCTTGACCATCTTTCTTAAGTTGGTATCTAATATTTTTGGGTTC
Found at i:46498 original size:20 final size:20
Alignment explanation
Indices: 46473--46512 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
46463 CTCTAGCTTC
46473 TTAGTCTAGTTACACACTCT
1 TTAGTCTAGTTACACACTCT
46493 TTAGTCTAGTTACACACTCT
1 TTAGTCTAGTTACACACTCT
46513 GAGATATTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.25, G:0.10, T:0.40
Consensus pattern (20 bp):
TTAGTCTAGTTACACACTCT
Found at i:50103 original size:47 final size:47
Alignment explanation
Indices: 50046--50141 Score: 192
Period size: 47 Copynumber: 2.0 Consensus size: 47
50036 ACGAGAATGA
50046 CAATCCGTTCATTATAGCTTCTTTGGCTTTAACATTTTAATTTATTT
1 CAATCCGTTCATTATAGCTTCTTTGGCTTTAACATTTTAATTTATTT
50093 CAATCCGTTCATTATAGCTTCTTTGGCTTTAACATTTTAATTTATTT
1 CAATCCGTTCATTATAGCTTCTTTGGCTTTAACATTTTAATTTATTT
50140 CA
1 CA
50142 TTTTCCTAGG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 49 1.00
ACGTcount: A:0.24, C:0.18, G:0.08, T:0.50
Consensus pattern (47 bp):
CAATCCGTTCATTATAGCTTCTTTGGCTTTAACATTTTAATTTATTT
Found at i:58297 original size:53 final size:53
Alignment explanation
Indices: 58217--58324 Score: 216
Period size: 53 Copynumber: 2.0 Consensus size: 53
58207 AGAGAAACGC
58217 GTTCATCAAGTCATGCTTTCCTGCATAGTAAAAGTGATGCTTCAATTGATTGT
1 GTTCATCAAGTCATGCTTTCCTGCATAGTAAAAGTGATGCTTCAATTGATTGT
58270 GTTCATCAAGTCATGCTTTCCTGCATAGTAAAAGTGATGCTTCAATTGATTGT
1 GTTCATCAAGTCATGCTTTCCTGCATAGTAAAAGTGATGCTTCAATTGATTGT
58323 GT
1 GT
58325 AGAAAAGCAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 55 1.00
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.38
Consensus pattern (53 bp):
GTTCATCAAGTCATGCTTTCCTGCATAGTAAAAGTGATGCTTCAATTGATTGT
Found at i:67915 original size:17 final size:17
Alignment explanation
Indices: 67887--67927 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
67877 TTTCTTCATA
*
67887 TCTTTATTATTTTATTAT
1 TCTTTATCATTTT-TTAT
67905 T-TTTATCATTTTTTAT
1 TCTTTATCATTTTTTAT
67921 TCTTTAT
1 TCTTTAT
67928 TGGTTTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 5 0.24
17 15 0.71
18 1 0.05
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (17 bp):
TCTTTATCATTTTTTAT
Found at i:68369 original size:16 final size:16
Alignment explanation
Indices: 68350--68393 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
68340 TGAATAGGGT
68350 TGTAATAGAATAAAAC
1 TGTAATAGAATAAAAC
* *
68366 TGTAATGGAATAAAAT
1 TGTAATAGAATAAAAC
68382 TGTAATA-AATAA
1 TGTAATAGAATAA
68394 TTCAGTTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
15 5 0.20
16 20 0.80
ACGTcount: A:0.55, C:0.02, G:0.14, T:0.30
Consensus pattern (16 bp):
TGTAATAGAATAAAAC
Found at i:72197 original size:31 final size:31
Alignment explanation
Indices: 72131--72190 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
72121 AAAAAAACTT
*
72131 AATAGCCCAATGACTTAAATGAAAACTTTCA
1 AATAGCCCAATGACTTAAATAAAAACTTTCA
* * *
72162 AATAGCTCAGTGATTTAAATAAAAACTTT
1 AATAGCCCAATGACTTAAATAAAAACTTT
72191 TGAATAGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.45, C:0.15, G:0.10, T:0.30
Consensus pattern (31 bp):
AATAGCCCAATGACTTAAATAAAAACTTTCA
Found at i:73234 original size:29 final size:32
Alignment explanation
Indices: 73185--73243 Score: 88
Period size: 30 Copynumber: 1.9 Consensus size: 32
73175 AAATCAAATC
*
73185 AAATCAAAATTTCATGTATAA-A-ATTATATA
1 AAATCAAAATTTCATATATAACATATTATATA
73215 AAATCAAAATTT-ATATATAACATATTATA
1 AAATCAAAATTTCATATATAACATATTATA
73244 CATTAGATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 7 0.27
30 13 0.50
31 6 0.23
ACGTcount: A:0.54, C:0.07, G:0.02, T:0.37
Consensus pattern (32 bp):
AAATCAAAATTTCATATATAACATATTATATA
Found at i:81957 original size:24 final size:23
Alignment explanation
Indices: 81935--81990 Score: 69
Period size: 22 Copynumber: 2.3 Consensus size: 23
81925 TAATTATTTT
81935 TAAAAAATTAATGATTAAAATTTAAC
1 TAAAAAA-TAATGA-TAAAATTT-AC
*
81961 TAAAAAATAATGATAAAATTAAC
1 TAAAAAATAATGATAAAATTTAC
81984 -AAAAAAT
1 TAAAAAAT
81991 TAAATTTGAC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 7 0.24
23 2 0.07
24 7 0.24
25 6 0.21
26 7 0.24
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.29
Consensus pattern (23 bp):
TAAAAAATAATGATAAAATTTAC
Found at i:81965 original size:25 final size:23
Alignment explanation
Indices: 81936--81993 Score: 82
Period size: 23 Copynumber: 2.4 Consensus size: 23
81926 AATTATTTTT
81936 AAAAAATTAATGATTAAAATTTAAC
1 AAAAAATTAATGA-TAAAA-TTAAC
81961 TAAAAAA-TAATGATAAAATTAAC
1 -AAAAAATTAATGATAAAATTAAC
81984 AAAAAATTAA
1 AAAAAATTAA
81994 ATTTGACATT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
22 6 0.19
23 8 0.26
24 5 0.16
25 6 0.19
26 6 0.19
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.28
Consensus pattern (23 bp):
AAAAAATTAATGATAAAATTAAC
Found at i:96949 original size:29 final size:29
Alignment explanation
Indices: 96886--96976 Score: 103
Period size: 29 Copynumber: 3.0 Consensus size: 29
96876 ATATCAAAAT
* * * *
96886 TATACATGAACTATGATTTAATGTGCAATTG
1 TATACATGAATTTTGATTT--TGTGTAATTC
96917 TATACATGAATTTTGATTTTGTGTAATTC
1 TATACATGAATTTTGATTTTGTGTAATTC
96946 TATACATGAAATTTTGA-TTTGATGTAATTC
1 TATACATG-AATTTTGATTTTG-TGTAATTC
96976 T
1 T
96977 TGTACATTTT
Statistics
Matches: 54, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
29 20 0.37
30 17 0.31
31 17 0.31
ACGTcount: A:0.32, C:0.08, G:0.14, T:0.46
Consensus pattern (29 bp):
TATACATGAATTTTGATTTTGTGTAATTC
Found at i:97175 original size:29 final size:30
Alignment explanation
Indices: 97097--97188 Score: 98
Period size: 31 Copynumber: 3.1 Consensus size: 30
97087 GATTACATCA
*
97097 AAATTAAAGTTTCAAGTATACATTTGAACC
1 AAATTAAAGTTTCAAGTATACAATTGAACC
* * * *
97127 ACAATTAGAGTTTCACGTATATAATTGCACC
1 A-AATTAAAGTTTCAAGTATACAATTGAACC
* *
97158 AAATTAAAG-TTCATGTATAC-ATTAAACC
1 AAATTAAAGTTTCAAGTATACAATTGAACC
97186 AAA
1 AAA
97189 GTTCATGCAT
Statistics
Matches: 51, Mismatches: 10, Indels: 4
0.78 0.15 0.06
Matches are distributed among these distances:
28 9 0.18
29 9 0.18
30 8 0.16
31 25 0.49
ACGTcount: A:0.43, C:0.15, G:0.10, T:0.32
Consensus pattern (30 bp):
AAATTAAAGTTTCAAGTATACAATTGAACC
Found at i:99397 original size:24 final size:25
Alignment explanation
Indices: 99345--99394 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
99335 TTGATGTGAA
**
99345 AAAAAAAAAATAGTTTAAAAAATAT
1 AAAAAAAAAATAGAGTAAAAAATAT
*
99370 AAAAAAAAATTAGAGTAATAAAATA
1 AAAAAAAAAATAGAGTAA-AAAATA
99395 AAATTACATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 15 0.71
26 6 0.29
ACGTcount: A:0.72, C:0.00, G:0.06, T:0.22
Consensus pattern (25 bp):
AAAAAAAAAATAGAGTAAAAAATAT
Found at i:105196 original size:28 final size:29
Alignment explanation
Indices: 105165--105234 Score: 106
Period size: 28 Copynumber: 2.4 Consensus size: 29
105155 TTTAACTAAT
* *
105165 ATTTTTTAAATAATTTTTATGA-TTTTTA
1 ATTTTTAAAATAATTTTTATAATTTTTTA
105193 ATTTTTAAAATAATTTTTATAATTTTTTTA
1 ATTTTTAAAATAATTTTTATAA-TTTTTTA
105223 ATTTTTAAAATA
1 ATTTTTAAAATA
105235 TAAAAATTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
28 20 0.53
30 18 0.47
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.61
Consensus pattern (29 bp):
ATTTTTAAAATAATTTTTATAATTTTTTA
Found at i:105216 original size:9 final size:9
Alignment explanation
Indices: 105174--105229 Score: 53
Period size: 9 Copynumber: 6.1 Consensus size: 9
105164 TATTTTTTAA
105174 ATAATTTTT
1 ATAATTTTT
*
105183 ATGA-TTTT
1 ATAATTTTT
105191 -TAATTTTT
1 ATAATTTTT
105199 AAAATAATTTTT
1 ---ATAATTTTT
105211 ATAATTTTT
1 ATAATTTTT
*
105220 TTAATTTTT
1 ATAATTTTT
105229 A
1 A
105230 AAATATAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
7 2 0.05
8 8 0.21
9 20 0.53
12 8 0.21
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (9 bp):
ATAATTTTT
Found at i:105379 original size:17 final size:18
Alignment explanation
Indices: 105359--105396 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
105349 AAAAAAACAT
*
105359 AAATTTAAAAACTAAA-A
1 AAATTGAAAAACTAAATA
*
105376 AAATTGAAAAATTAAATA
1 AAATTGAAAAACTAAATA
105394 AAA
1 AAA
105397 AACTAAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.24
Consensus pattern (18 bp):
AAATTGAAAAACTAAATA
Found at i:111900 original size:70 final size:67
Alignment explanation
Indices: 111784--111913 Score: 170
Period size: 70 Copynumber: 1.9 Consensus size: 67
111774 AACGATATAG
* * * * *
111784 TGGTTTTGCCTTTTGACTTAATAAGTAAATATTTATCAAAATGACGTAATTTTACCTTTTAATTT
1 TGGTTTTGACTTTTAACTTAAAAAGTAAACATTTATCAAAACGACGTAATTTTACCTTTTAATTT
111849 AA
66 AA
* *
111851 TGGTTTTGACTTTTAACTTTACAAAAGATAAACATTTATCAAAACGACGTAGTTTTACTTTTT
1 TGGTTTTGACTTTTAAC-TTA-AAAAG-TAAACATTTATCAAAACGACGTAATTTTACCTTTT
111914 TCTTATTCAA
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
67 15 0.28
68 3 0.06
69 4 0.08
70 31 0.58
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.45
Consensus pattern (67 bp):
TGGTTTTGACTTTTAACTTAAAAAGTAAACATTTATCAAAACGACGTAATTTTACCTTTTAATTT
AA
Found at i:116169 original size:2 final size:2
Alignment explanation
Indices: 116164--116189 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
116154 AAAAAAAAAA
116164 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
116190 TGTTGCATTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:116269 original size:21 final size:21
Alignment explanation
Indices: 116228--116292 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 21
116218 TTTAAAAATT
* * *
116228 AAAAAAA-TATCATTTTTTAA
1 AAAAAAATTATAAATTTATAA
*
116248 AAAAAAATTATAAATTTGTAA
1 AAAAAAATTATAAATTTATAA
* **
116269 AATATTATTA-AAATTTATAA
1 AAAAAAATTATAAATTTATAA
116289 AAAA
1 AAAA
116293 TATTAAATAA
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
20 19 0.53
21 17 0.47
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (21 bp):
AAAAAAATTATAAATTTATAA
Found at i:116270 original size:19 final size:21
Alignment explanation
Indices: 116243--116306 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 21
116233 AATATCATTT
*
116243 TTTAAAAAAAAATTA-T-AAA
1 TTTATAAAAAAATTATTAAAA
* *
116262 TTTGT-AAAATATTATTAAAA
1 TTTATAAAAAAATTATTAAAA
*
116282 TTTATAAAAAATATTAAATAAAA
1 TTTATAAAAAA-ATT-ATTAAAA
116305 TT
1 TT
116307 CAAAAAGTTA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
18 8 0.24
19 4 0.12
20 7 0.21
21 4 0.12
22 3 0.09
23 8 0.24
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (21 bp):
TTTATAAAAAAATTATTAAAA
Found at i:116270 original size:20 final size:19
Alignment explanation
Indices: 116243--116299 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
116233 AATATCATTT
*
116243 TTTA-AAAAAAAATTATAAA
1 TTTATAAAAAATATTA-AAA
* *
116262 TTTGTAAAATATTATTAAAA
1 TTTATAAAA-AATATTAAAA
116282 TTTATAAAAAATATTAAA
1 TTTATAAAAAATATTAAA
116300 TAAAATTCAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
19 11 0.35
20 15 0.48
21 5 0.16
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (19 bp):
TTTATAAAAAATATTAAAA
Found at i:116312 original size:22 final size:22
Alignment explanation
Indices: 116267--116312 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
116257 ATAAATTTGT
* *
116267 AAAATATTATTAAAATTTATAA
1 AAAATATTAATAAAATTCATAA
116289 AAAATATTAAATAAAATTCA-AA
1 AAAATATT-AATAAAATTCATAA
116311 AA
1 AA
116313 GTTAAAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (22 bp):
AAAATATTAATAAAATTCATAA
Found at i:116336 original size:16 final size:18
Alignment explanation
Indices: 116298--116336 Score: 50
Period size: 16 Copynumber: 2.4 Consensus size: 18
116288 AAAAATATTA
116298 AATAAAATTCAAAAAGTT
1 AATAAAATTCAAAAAGTT
116316 -A-AAAATT-AAAAA-TT
1 AATAAAATTCAAAAAGTT
116330 AATAAAA
1 AATAAAA
116337 ATCATTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 6
0.76 0.00 0.24
Matches are distributed among these distances:
14 2 0.11
15 6 0.32
16 10 0.53
17 1 0.05
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.26
Consensus pattern (18 bp):
AATAAAATTCAAAAAGTT
Found at i:117641 original size:3 final size:3
Alignment explanation
Indices: 117633--117664 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
117623 TATACTTCCT
117633 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
117665 TTTTTTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:117716 original size:2 final size:2
Alignment explanation
Indices: 117711--117736 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
117701 TTTCTTTTTC
117711 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
117737 GTGTGTGTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:122346 original size:6 final size:6
Alignment explanation
Indices: 122332--122364 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
122322 AAAAGTGATG
*
122332 CCCTTC CCCTCC CCCTCC CCCTCC CCCTCC CCC
1 CCCTCC CCCTCC CCCTCC CCCTCC CCCTCC CCC
122365 CTGTATTTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.82, G:0.00, T:0.18
Consensus pattern (6 bp):
CCCTCC
Found at i:127563 original size:24 final size:25
Alignment explanation
Indices: 127536--127603 Score: 97
Period size: 24 Copynumber: 2.8 Consensus size: 25
127526 ATCTTTCAGT
127536 TAAACTCTGTTTAATTT-TTTCAAA
1 TAAACTCTGTTTAATTTGTTTCAAA
* *
127560 TAAACTCAGTTT-ATTTGTTTCAAT
1 TAAACTCTGTTTAATTTGTTTCAAA
127584 TAAACTCTGTTT-ATTTGTTT
1 TAAACTCTGTTTAATTTGTTT
127604 GAGTCAAACT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
23 4 0.10
24 36 0.90
ACGTcount: A:0.28, C:0.12, G:0.07, T:0.53
Consensus pattern (25 bp):
TAAACTCTGTTTAATTTGTTTCAAA
Found at i:127612 original size:24 final size:24
Alignment explanation
Indices: 127537--127615 Score: 90
Period size: 24 Copynumber: 3.3 Consensus size: 24
127527 TCTTTCAGTT
127537 AAACTCTGTTTAATTT-TTTCAAAT-
1 AAACTCTGTTT-ATTTGTTTC-AATC
* *
127561 AAACTCAGTTTATTTGTTTCAATT
1 AAACTCTGTTTATTTGTTTCAATC
* *
127585 AAACTCTGTTTATTTGTTTGAGTC
1 AAACTCTGTTTATTTGTTTCAATC
127609 AAACTCT
1 AAACTCT
127616 TATTAGTCTA
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
23 7 0.15
24 41 0.85
ACGTcount: A:0.29, C:0.14, G:0.09, T:0.48
Consensus pattern (24 bp):
AAACTCTGTTTATTTGTTTCAATC
Found at i:131958 original size:6 final size:6
Alignment explanation
Indices: 131916--131954 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
131906 ACCTAACAGA
*
131916 TGCGGC TGCGGC TGCGGC TGCGGC TGCGGC TGCTGC TGC
1 TGCGGC TGCGGC TGCGGC TGCGGC TGCGGC TGCGGC TGC
131955 TGCTTTTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.00, C:0.33, G:0.46, T:0.21
Consensus pattern (6 bp):
TGCGGC
Found at i:143667 original size:39 final size:39
Alignment explanation
Indices: 143619--143695 Score: 109
Period size: 39 Copynumber: 2.0 Consensus size: 39
143609 TAAAAAGACC
* * * *
143619 ACTTATTGAAGATTTATATTGCCTCTAGAAATGTGGACA
1 ACTTATTGAAGATTTACATAGCCCCTAGAAATATGGACA
*
143658 ACTTTTTGAAGATTTACATAGCCCCTAGAAATATGGAC
1 ACTTATTGAAGATTTACATAGCCCCTAGAAATATGGAC
143696 GAGAATTCAG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Consensus pattern (39 bp):
ACTTATTGAAGATTTACATAGCCCCTAGAAATATGGACA
Found at i:161883 original size:42 final size:42
Alignment explanation
Indices: 161836--161927 Score: 175
Period size: 42 Copynumber: 2.2 Consensus size: 42
161826 ATTCGAGTTT
*
161836 GAACTCAAGCTCGATTAAACTCGTTTATTAATGATTAAACAG
1 GAACTCAAGCTCGATTAAACTCATTTATTAATGATTAAACAG
161878 GAACTCAAGCTCGATTAAACTCATTTATTAATGATTAAACAG
1 GAACTCAAGCTCGATTAAACTCATTTATTAATGATTAAACAG
161920 GAACTCAA
1 GAACTCAA
161928 ATTAAAATTA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.29
Consensus pattern (42 bp):
GAACTCAAGCTCGATTAAACTCATTTATTAATGATTAAACAG
Found at i:174173 original size:9 final size:9
Alignment explanation
Indices: 174159--174185 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
174149 CAAATTTATA
174159 AAAAAAAAG
1 AAAAAAAAG
174168 AAAAAAAAG
1 AAAAAAAAG
174177 AAAAAAAAG
1 AAAAAAAAG
174186 TCTTGTTTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:182559 original size:30 final size:30
Alignment explanation
Indices: 182492--182628 Score: 120
Period size: 30 Copynumber: 4.6 Consensus size: 30
182482 TTATAGATGT
* *
182492 TTAAAAGTTAAATTTATTAAAGTTTTAAA-A
1 TTAAAAATTAAATTTA-TAAAATTTTAAATA
*
182522 TT-CAAATTCAAA-TTAT-AAATTTATAAATA
1 TTAAAAATT-AAATTTATAAAATTT-TAAATA
** **
182551 TTAAAAATTAAATTTATCGAATTTTTTATA
1 TTAAAAATTAAATTTATAAAATTTTAAATA
* * *
182581 TTTAAGATTAAATTTATAAAATATGTAAATA
1 TTAAAAATTAAATTTATAAAAT-TTTAAATA
182612 TTAAAAATTAAATTTAT
1 TTAAAAATTAAATTTAT
182629 TTTTATATTA
Statistics
Matches: 84, Mismatches: 16, Indels: 13
0.74 0.14 0.12
Matches are distributed among these distances:
27 5 0.06
28 5 0.06
29 13 0.15
30 36 0.43
31 25 0.30
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.45
Consensus pattern (30 bp):
TTAAAAATTAAATTTATAAAATTTTAAATA
Found at i:182564 original size:59 final size:61
Alignment explanation
Indices: 182492--182629 Score: 165
Period size: 59 Copynumber: 2.3 Consensus size: 61
182482 TTATAGATGT
* *
182492 TTAAAAGTTAAATTTATTAAAGTTTTAAAATTCAA-ATTCAAA-TTAT-AAATTTATAAATA
1 TTAAAAATTAAATTTATTAAAGTTTTAAAATTCAAGATT-AAATTTATAAAATATATAAATA
** * * * * *
182551 TTAAAAATTAAATTTATCGAATTTTTTATATTTAAGATTAAATTTATAAAATATGTAAATA
1 TTAAAAATTAAATTTATTAAAGTTTTAAAATTCAAGATTAAATTTATAAAATATATAAATA
182612 TTAAAAATTAAATTTATT
1 TTAAAAATTAAATTTATT
182630 TTTATATTAA
Statistics
Matches: 66, Mismatches: 10, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
59 31 0.47
60 7 0.11
61 28 0.42
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (61 bp):
TTAAAAATTAAATTTATTAAAGTTTTAAAATTCAAGATTAAATTTATAAAATATATAAATA
Found at i:182733 original size:3 final size:3
Alignment explanation
Indices: 182720--182751 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
182710 TTGGTGATTA
182720 AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
182752 TGAATGACTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:182994 original size:2 final size:2
Alignment explanation
Indices: 182987--183013 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
182977 TATTATAAGC
182987 AG 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 AG A
183014 AGGTCAGACG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:185104 original size:16 final size:15
Alignment explanation
Indices: 185067--185102 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
185057 CAAAATCAAG
185067 ATTTTTACAACATTC
1 ATTTTTACAACATTC
**
185082 ATTTTTACATTATTC
1 ATTTTTACAACATTC
185097 ATTTTT
1 ATTTTT
185103 TATTAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.28, C:0.14, G:0.00, T:0.58
Consensus pattern (15 bp):
ATTTTTACAACATTC
Found at i:187132 original size:23 final size:23
Alignment explanation
Indices: 187094--187183 Score: 103
Period size: 23 Copynumber: 3.9 Consensus size: 23
187084 CGCTTTCTAT
*
187094 TTAGCACTTC-TCGTGCTTTCTTA
1 TTAGCACTTCGT-GTGCTCTCTTA
187117 TTAGCACTTCGTGTGCTCTCTTA
1 TTAGCACTTCGTGTGCTCTCTTA
* * *
187140 TTAACACTTTGTGTACTCTCTGT-
1 TTAGCACTTCGTGTGCTCTCT-TA
*
187163 TTAGCACTTTGTGTGCTCTCT
1 TTAGCACTTCGTGTGCTCTCT
187184 GTTGCTCAGC
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
23 57 0.97
24 2 0.03
ACGTcount: A:0.13, C:0.24, G:0.16, T:0.47
Consensus pattern (23 bp):
TTAGCACTTCGTGTGCTCTCTTA
Found at i:187184 original size:23 final size:23
Alignment explanation
Indices: 187117--187234 Score: 116
Period size: 23 Copynumber: 5.1 Consensus size: 23
187107 TGCTTTCTTA
*
187117 TTAGCACTTCGTGTGCTCTCT-T
1 TTAGCACTTTGTGTGCTCTCTGT
* *
187139 ATTAACACTTTGTGTACTCTCTGT
1 -TTAGCACTTTGTGTGCTCTCTGT
187163 TTAGCACTTTGTGTGCTCTCTGT
1 TTAGCACTTTGTGTGCTCTCTGT
* *
187186 TGCTCAGCAC-TTATGTGCTCTTTGT
1 T--T-AGCACTTTGTGTGCTCTCTGT
* *
187211 TTAGTACTTTG-GTACTCTCTGT
1 TTAGCACTTTGTGTGCTCTCTGT
187233 TT
1 TT
187235 GTTCTGTTTA
Statistics
Matches: 79, Mismatches: 11, Indels: 11
0.78 0.11 0.11
Matches are distributed among these distances:
22 15 0.19
23 43 0.54
24 1 0.01
25 15 0.19
26 5 0.06
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (23 bp):
TTAGCACTTTGTGTGCTCTCTGT
Found at i:194318 original size:26 final size:27
Alignment explanation
Indices: 194289--194339 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
194279 TTCATATATT
*
194289 TTATGTTTAAATATTT-TATTGAAGAA
1 TTATGTTTAAATATTTAAATTGAAGAA
*
194315 TTATTTTTAAATATTTAAATTGAAG
1 TTATGTTTAAATATTTAAATTGAAG
194340 CGGAACGGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 15 0.68
27 7 0.32
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.51
Consensus pattern (27 bp):
TTATGTTTAAATATTTAAATTGAAGAA
Found at i:194633 original size:26 final size:28
Alignment explanation
Indices: 194597--194653 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
194587 AAGTTCCCAA
* *
194597 TTTTTTA-TTTT-ATTACTAGTATATGT
1 TTTTTTATTTTTGAATAATAGTATATGT
*
194623 TTTTTTCTTTTTGAATAATAGTATATGT
1 TTTTTTATTTTTGAATAATAGTATATGT
194651 TTT
1 TTT
194654 CATTTTATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 6 0.23
27 4 0.15
28 16 0.62
ACGTcount: A:0.23, C:0.04, G:0.09, T:0.65
Consensus pattern (28 bp):
TTTTTTATTTTTGAATAATAGTATATGT
Found at i:195185 original size:21 final size:22
Alignment explanation
Indices: 195160--195224 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
195150 AAAATTTATA
*
195160 TTATTGTTTTGGTT-TTATTTT
1 TTATTGTTTTGGTTGCTATTTT
* *
195181 TTATTGCTTCGGTTGCTATTTT
1 TTATTGTTTTGGTTGCTATTTT
* *
195203 TTACTGTTTTGGTTGCTGTTTT
1 TTATTGTTTTGGTTGCTATTTT
195225 GGTTTTTTTT
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
21 12 0.33
22 24 0.67
ACGTcount: A:0.08, C:0.08, G:0.18, T:0.66
Consensus pattern (22 bp):
TTATTGTTTTGGTTGCTATTTT
Found at i:195265 original size:12 final size:12
Alignment explanation
Indices: 195248--195295 Score: 62
Period size: 12 Copynumber: 4.1 Consensus size: 12
195238 GTTTTGATGC
195248 TGTTGTTTTTGT
1 TGTTGTTTTTGT
*
195260 TGTTGTTTTTAT
1 TGTTGTTTTTGT
*
195272 TGTTG-TTTTGC
1 TGTTGTTTTTGT
*
195283 TGTTATTTTTGT
1 TGTTGTTTTTGT
195295 T
1 T
195296 ACTATTTTGG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
11 8 0.27
12 22 0.73
ACGTcount: A:0.04, C:0.02, G:0.21, T:0.73
Consensus pattern (12 bp):
TGTTGTTTTTGT
Found at i:196935 original size:22 final size:24
Alignment explanation
Indices: 196910--196976 Score: 68
Period size: 25 Copynumber: 2.7 Consensus size: 24
196900 ATATTTTCAA
196910 AAAATATATAATAATAA-AA-TTT
1 AAAATATATAATAATAATAATTTT
196932 AAAATATATGAAAATAATTAAATAATTTT
1 AAAATATAT---AATAA-T-AATAATTTT
196961 AAAA-ATATAATAATAA
1 AAAATATATAATAATAA
196977 GTTTAAATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
22 9 0.24
23 2 0.05
24 1 0.03
25 10 0.26
26 1 0.03
27 2 0.05
28 6 0.16
29 7 0.18
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.34
Consensus pattern (24 bp):
AAAATATATAATAATAATAATTTT
Found at i:197581 original size:6 final size:6
Alignment explanation
Indices: 197570--197614 Score: 54
Period size: 6 Copynumber: 7.3 Consensus size: 6
197560 AGCAACAGAA
* * *
197570 GAGAGG GAGAGG GAGAGG GAGACG GAGACG GAGACG GAGACGG GA
1 GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGA-GG GA
197615 CGGTGGTGGA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
6 33 0.92
7 3 0.08
ACGTcount: A:0.33, C:0.09, G:0.58, T:0.00
Consensus pattern (6 bp):
GAGAGG
Found at i:197587 original size:12 final size:12
Alignment explanation
Indices: 197570--197614 Score: 63
Period size: 12 Copynumber: 3.7 Consensus size: 12
197560 AGCAACAGAA
*
197570 GAGAGGGAGAGG
1 GAGAGGGAGACG
197582 GAGAGGGAGACG
1 GAGAGGGAGACG
*
197594 GAGACGGAGACG
1 GAGAGGGAGACG
197606 GAGACGGGA
1 GAGA-GGGA
197615 CGGTGGTGGA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
12 26 0.90
13 3 0.10
ACGTcount: A:0.33, C:0.09, G:0.58, T:0.00
Consensus pattern (12 bp):
GAGAGGGAGACG
Found at i:197596 original size:18 final size:18
Alignment explanation
Indices: 197570--197617 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
197560 AGCAACAGAA
* * *
197570 GAGAGGGAGAGGGAGAGG
1 GAGACGGAGACGGAGACG
197588 GAGACGGAGACGGAGACG
1 GAGACGGAGACGGAGACG
197606 GAGACGG-GACGG
1 GAGACGGAGACGG
197618 TGGTGGAAGG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 5 0.19
18 22 0.81
ACGTcount: A:0.31, C:0.10, G:0.58, T:0.00
Consensus pattern (18 bp):
GAGACGGAGACGGAGACG
Found at i:197671 original size:25 final size:22
Alignment explanation
Indices: 197637--197683 Score: 67
Period size: 25 Copynumber: 2.0 Consensus size: 22
197627 GGAGACGGGG
197637 TTATTTTTATTTAATATTAATATAA
1 TTATTTTTA-TTAA-A-TAATATAA
197662 TTATTTTTATTAAATAATATAA
1 TTATTTTTATTAAATAATATAA
197684 AATTTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 8 0.36
23 1 0.05
24 4 0.18
25 9 0.41
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TTATTTTTATTAAATAATATAA
Found at i:207142 original size:36 final size:33
Alignment explanation
Indices: 207102--207173 Score: 81
Period size: 35 Copynumber: 2.1 Consensus size: 33
207092 AAGATGACTG
207102 TATAAAAATTTTCAATAAAAAAATAAATTAAAATAA
1 TATAAAAATTTT-AATAAAAAAATAAA--AAAATAA
* ** *
207138 TATAAATATTTTTTTAAAAAATTAAAAAAATAA
1 TATAAAAATTTTAATAAAAAAATAAAAAAATAA
207171 TAT
1 TAT
207174 GAGCATGCTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
33 10 0.31
35 11 0.34
36 11 0.34
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.36
Consensus pattern (33 bp):
TATAAAAATTTTAATAAAAAAATAAAAAAATAA
Found at i:208023 original size:29 final size:29
Alignment explanation
Indices: 207949--208024 Score: 100
Period size: 29 Copynumber: 2.6 Consensus size: 29
207939 CGGAGGATTT
* **
207949 TATTTTATATATTTTTTCGAATATTTATG
1 TATTTTATATTTTTTTTTAAATATTTATG
*
207978 TATTTT-TATTATATTTTTAAATATTTATG
1 TATTTTATATT-TTTTTTTAAATATTTATG
208007 TATTTTATATTTTTTTTT
1 TATTTTATATTTTTTTTT
208025 TGAATTTTCT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
28 3 0.08
29 33 0.82
30 4 0.10
ACGTcount: A:0.26, C:0.01, G:0.04, T:0.68
Consensus pattern (29 bp):
TATTTTATATTTTTTTTTAAATATTTATG
Found at i:208473 original size:13 final size:14
Alignment explanation
Indices: 208443--208490 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 14
208433 AAAAATATTT
208443 TTTAATATTTAAATAA
1 TTTAATATTT--ATAA
208459 TTTAATA-TTATAA
1 TTTAATATTTATAA
* *
208472 TTTTATATTTTTAA
1 TTTAATATTTATAA
208486 TTTAA
1 TTTAA
208491 ATAATTTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
13 10 0.36
14 9 0.32
15 2 0.07
16 7 0.25
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TTTAATATTTATAA
Found at i:212193 original size:29 final size:29
Alignment explanation
Indices: 212127--212193 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
212117 GGGATTTAGG
* *
212127 GGTCAAAATTGAAATTTTTGGAAAATTTA
1 GGTCAAAATTCAAACTTTTGGAAAATTTA
* *
212156 GAATTAAAA-TCAAACTTTTGGAAAATTTGA
1 G-GTCAAAATTCAAACTTTTGGAAAATTT-A
212186 GGTCAAAA
1 GGTCAAAA
212194 ATGTGATTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
29 23 0.77
30 7 0.23
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (29 bp):
GGTCAAAATTCAAACTTTTGGAAAATTTA
Found at i:212205 original size:30 final size:29
Alignment explanation
Indices: 212171--212381 Score: 146
Period size: 30 Copynumber: 7.1 Consensus size: 29
212161 AAAATCAAAC
212171 TTTTGGAAAATTTGAGGTCAAAAATGTGAT
1 TTTTGGAAAATTTGAGGTC-AAAATGTGAT
*
212201 TTTTGG-AAATTTGGGGGTCAAAATGTGAT
1 TTTTGGAAAATTT-GAGGTCAAAATGTGAT
* *
212230 TTTTGGAAAGTTCGTG-GGTTAAAA--TGAT
1 TTTTGGAAAATT--TGAGGTCAAAATGTGAT
* * *
212258 TTTTGGAAAGTTTTGGGGTCAAAATGTAAT
1 TTTTGGAAA-ATTTGAGGTCAAAATGTGAT
* * *
212288 TTTTGGAAAGTTTGATGATCAAAATGTAATT
1 TTTTGGAAAATTTGA-GGTCAAAATGTGA-T
* * *
212319 TTTTTG-AAGTTTAAGGGTCAAAATGTGAT
1 TTTTGGAAAATTTGA-GGTCAAAATGTGAT
*** *
212348 TTTCATAAAGTTT-AGGGATCAAAATGTGAT
1 TTTTGGAAAATTTGA-GG-TCAAAATGTGAT
212378 TTTT
1 TTTT
212382 AGACAAAATA
Statistics
Matches: 151, Mismatches: 18, Indels: 24
0.78 0.09 0.12
Matches are distributed among these distances:
27 2 0.01
28 20 0.13
29 36 0.24
30 85 0.56
31 7 0.05
32 1 0.01
ACGTcount: A:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (29 bp):
TTTTGGAAAATTTGAGGTCAAAATGTGAT
Found at i:212342 original size:60 final size:59
Alignment explanation
Indices: 212171--212381 Score: 198
Period size: 60 Copynumber: 3.6 Consensus size: 59
212161 AAAATCAAAC
* * * *
212171 TTTTGGAAAATTTGA-GGTCAAAAATGTGATTTTTGGAAATTTGGGGGTCAAAATGTGAT
1 TTTTGGAAAGTTTGATGATC-AAAATGTGATTTTTGGAAGTTTAGGGGTCAAAATGTGAT
* * * * *
212230 TTTTGGAAAGTTCG-TGGGTTAAAA--TGATTTTTGGAAAGTTTTGGGGTCAAAATGTAAT
1 TTTTGGAAAGTTTGAT-GATCAAAATGTGATTTTTGG-AAGTTTAGGGGTCAAAATGTGAT
* * *
212288 TTTTGGAAAGTTTGATGATCAAAATGTAATTTTTTTGAAGTTTAAGGGTCAAAATGTGAT
1 TTTTGGAAAGTTTGATGATCAAAATGTGA-TTTTTGGAAGTTTAGGGGTCAAAATGTGAT
*** *
212348 TTTCATAAAGTTT-AGGGATCAAAATGTGATTTTT
1 TTTTGGAAAGTTTGA-TGATCAAAATGTGATTTTT
212382 AGACAAAATA
Statistics
Matches: 125, Mismatches: 19, Indels: 16
0.78 0.12 0.10
Matches are distributed among these distances:
57 10 0.08
58 39 0.31
59 23 0.18
60 47 0.38
61 6 0.05
ACGTcount: A:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (59 bp):
TTTTGGAAAGTTTGATGATCAAAATGTGATTTTTGGAAGTTTAGGGGTCAAAATGTGAT
Found at i:213384 original size:17 final size:19
Alignment explanation
Indices: 213361--213405 Score: 60
Period size: 17 Copynumber: 2.5 Consensus size: 19
213351 TCAACTTTCT
213361 TTTATTTATTTA-TTAATA
1 TTTATTTATTTATTTAATA
*
213379 -TTATTTA-ATATTTAATA
1 TTTATTTATTTATTTAATA
213396 TTTATTTATT
1 TTTATTTATT
213406 AAAACGTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
16 2 0.09
17 13 0.59
18 7 0.32
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTATTTATTTATTTAATA
Found at i:217140 original size:44 final size:45
Alignment explanation
Indices: 217068--217166 Score: 121
Period size: 44 Copynumber: 2.2 Consensus size: 45
217058 AATTACTAAT
* *
217068 TAATCCTTAAATTTTCTTAACCTTTCTTA-TTTAGACTACACATTC
1 TAATTCTTAAATTTTCTTAACCTTTCTTATTTTA-ACCACACATTC
* * *
217113 TAATTCTTAATTTTTCTTAATC-TTCTTATTTTAACCACATATTC
1 TAATTCTTAAATTTTCTTAACCTTTCTTATTTTAACCACACATTC
*
217157 TAACTCTTAA
1 TAATTCTTAA
217167 CTCGACACTG
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
44 24 0.51
45 23 0.49
ACGTcount: A:0.29, C:0.20, G:0.01, T:0.49
Consensus pattern (45 bp):
TAATTCTTAAATTTTCTTAACCTTTCTTATTTTAACCACACATTC
Found at i:217815 original size:23 final size:23
Alignment explanation
Indices: 217714--217815 Score: 89
Period size: 23 Copynumber: 4.4 Consensus size: 23
217704 ACACTAGCGC
*
217714 GCTCTCTGTTTAGCAC-GTCTCGT
1 GCTCTCTGTTTAGCACTGTGT-GT
** * *
217737 GCTCTCTGACTAACACTTTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
* * *
217760 GCTCTCTGATTAGTACTTTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
* *
217783 ACTCTTTGTTTAGCACTGTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
*
217806 GCCCTCTGTT
1 GCTCTCTGTT
217816 ACCCAGCACT
Statistics
Matches: 62, Mismatches: 16, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
23 60 0.97
24 2 0.03
ACGTcount: A:0.12, C:0.25, G:0.21, T:0.43
Consensus pattern (23 bp):
GCTCTCTGTTTAGCACTGTGTGT
Found at i:219205 original size:2 final size:2
Alignment explanation
Indices: 219194--219225 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
219184 TCTACCTCTA
219194 AT AT -T 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 AT AT A
219226 AAGAAATCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:247030 original size:6 final size:6
Alignment explanation
Indices: 247014--247054 Score: 73
Period size: 6 Copynumber: 6.8 Consensus size: 6
247004 GATAACAGGT
*
247014 CTCCCA TTCCCA CTCCCA CTCCCA CTCCCA CTCCCA CTCCC
1 CTCCCA CTCCCA CTCCCA CTCCCA CTCCCA CTCCCA CTCCC
247055 TTTTCTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.15, C:0.66, G:0.00, T:0.20
Consensus pattern (6 bp):
CTCCCA
Found at i:252213 original size:17 final size:17
Alignment explanation
Indices: 252191--252223 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
252181 TTCTTAAATT
*
252191 TTTAAAAATTAAAAAAA
1 TTTAAAAAATAAAAAAA
252208 TTTAAAAAATAAAAAA
1 TTTAAAAAATAAAAAA
252224 TACTTAAAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
TTTAAAAAATAAAAAAA
Found at i:252232 original size:17 final size:17
Alignment explanation
Indices: 252192--252232 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
252182 TCTTAAATTT
*
252192 TTAAAAATTAAAAAAAT
1 TTAAAAATTAAAAAAAC
*
252209 TTAAAAAATAAAAAATAC
1 TTAAAAATTAAAAAA-AC
252227 TTAAAA
1 TTAAAA
252233 GTTCATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 14 0.67
18 7 0.33
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (17 bp):
TTAAAAATTAAAAAAAC
Found at i:252369 original size:15 final size:15
Alignment explanation
Indices: 252338--252387 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 15
252328 ATAAAATTTA
252338 TTTATTAAAATAATAAT
1 TTTA-TAAAA-AATAAT
252355 TTTATAAAAAATAAT
1 TTTATAAAAAATAAT
* *
252370 ATTATAATAAAACAAT
1 TTTATAA-AAAATAAT
252386 TT
1 TT
252388 AACGGGGAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
15 12 0.41
16 13 0.45
17 4 0.14
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (15 bp):
TTTATAAAAAATAAT
Found at i:252379 original size:18 final size:18
Alignment explanation
Indices: 252344--252381 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
252334 TTTATTTATT
*
252344 AAAATAATAATTTTATAA
1 AAAATAATAATTTAATAA
252362 AAAATAAT-ATTATAATAA
1 AAAATAATAATT-TAATAA
252380 AA
1 AA
252382 CAATTTAACG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 3 0.17
18 15 0.83
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
AAAATAATAATTTAATAA
Found at i:253066 original size:59 final size:62
Alignment explanation
Indices: 252983--253099 Score: 154
Period size: 59 Copynumber: 1.9 Consensus size: 62
252973 TTTTTTATTG
252983 AATTTTTAAGAAGTGAAATTAAATTGACAGAATAT-ATAAA-ATT-AAGGGTTAAATTTGTTA
1 AATTTTTAAGAAGTGAAATTAAATTGACAGAATATGA-AAACATTGAAGGGTTAAATTTGTTA
* * *
253043 AATTTTT-AGAA-TTAAGATTAAATTGATAGAATTTGAAAACATTGAAGGGTTAAATTT
1 AATTTTTAAGAAGTGAA-ATTAAATTGACAGAATATGAAAACATTGAAGGGTTAAATTT
253100 ATTATTATTC
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
58 3 0.06
59 23 0.46
60 11 0.22
61 13 0.26
ACGTcount: A:0.45, C:0.02, G:0.15, T:0.38
Consensus pattern (62 bp):
AATTTTTAAGAAGTGAAATTAAATTGACAGAATATGAAAACATTGAAGGGTTAAATTTGTTA
Found at i:254363 original size:102 final size:102
Alignment explanation
Indices: 254237--254440 Score: 408
Period size: 102 Copynumber: 2.0 Consensus size: 102
254227 CTTAAGCTCC
254237 CTTTGAATCTCATCACACCAACCGTGAAATGGAATCTGAGGAGTATATCCTCACTGAGGATAACT
1 CTTTGAATCTCATCACACCAACCGTGAAATGGAATCTGAGGAGTATATCCTCACTGAGGATAACT
254302 AATGGTGAGATCAACCAAAACCACCACAACCCTTATT
66 AATGGTGAGATCAACCAAAACCACCACAACCCTTATT
254339 CTTTGAATCTCATCACACCAACCGTGAAATGGAATCTGAGGAGTATATCCTCACTGAGGATAACT
1 CTTTGAATCTCATCACACCAACCGTGAAATGGAATCTGAGGAGTATATCCTCACTGAGGATAACT
254404 AATGGTGAGATCAACCAAAACCACCACAACCCTTATT
66 AATGGTGAGATCAACCAAAACCACCACAACCCTTATT
254441 TCTCACTGGA
Statistics
Matches: 102, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
102 102 1.00
ACGTcount: A:0.35, C:0.25, G:0.16, T:0.24
Consensus pattern (102 bp):
CTTTGAATCTCATCACACCAACCGTGAAATGGAATCTGAGGAGTATATCCTCACTGAGGATAACT
AATGGTGAGATCAACCAAAACCACCACAACCCTTATT
Found at i:254501 original size:6 final size:6
Alignment explanation
Indices: 254490--254518 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
254480 CCCAACCAGG
254490 TTTTAC TTTTAC TTTTAC TTTTAC TTTTA
1 TTTTAC TTTTAC TTTTAC TTTTAC TTTTA
254519 ACTCCTACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.14, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTTAC
Found at i:254901 original size:17 final size:16
Alignment explanation
Indices: 254879--254912 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
254869 TTTTTTTAAA
*
254879 AATAATTTATTATTTTT
1 AATAATTT-TAATTTTT
254896 AATAATTTTAATTTTT
1 AATAATTTTAATTTTT
254912 A
1 A
254913 TTTAACCTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
AATAATTTTAATTTTT
Found at i:262631 original size:59 final size:59
Alignment explanation
Indices: 262535--262652 Score: 227
Period size: 59 Copynumber: 2.0 Consensus size: 59
262525 TGACAGCTTC
*
262535 GGGGATGAAAAATGACAGCTTCGTTAAATTTGTAACGGAGAATTGTTACCGATGAATGT
1 GGGGATGAAAAATGACAGCTTCGTTAAATTTGAAACGGAGAATTGTTACCGATGAATGT
262594 GGGGATGAAAAATGACAGCTTCGTTAAATTTGAAACGGAGAATTGTTACCGATGAATGT
1 GGGGATGAAAAATGACAGCTTCGTTAAATTTGAAACGGAGAATTGTTACCGATGAATGT
262653 TTTATTATTT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.35, C:0.10, G:0.27, T:0.28
Consensus pattern (59 bp):
GGGGATGAAAAATGACAGCTTCGTTAAATTTGAAACGGAGAATTGTTACCGATGAATGT
Found at i:281474 original size:41 final size:41
Alignment explanation
Indices: 281417--281496 Score: 160
Period size: 41 Copynumber: 2.0 Consensus size: 41
281407 CTAGGAGTAA
281417 ATAATTTTAATTTTCTTTTTTAAAAATAGCTCTTGATGTAT
1 ATAATTTTAATTTTCTTTTTTAAAAATAGCTCTTGATGTAT
281458 ATAATTTTAATTTTCTTTTTTAAAAATAGCTCTTGATGT
1 ATAATTTTAATTTTCTTTTTTAAAAATAGCTCTTGATGT
281497 TTACACATGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.31, C:0.07, G:0.07, T:0.54
Consensus pattern (41 bp):
ATAATTTTAATTTTCTTTTTTAAAAATAGCTCTTGATGTAT
Found at i:285395 original size:15 final size:15
Alignment explanation
Indices: 285375--285428 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 15
285365 ATACTACAAA
285375 ATATTTATTATTAAT
1 ATATTTATTATTAAT
*
285390 ATATTTATAAATGTAAT
1 ATATTTAT-TAT-TAAT
*
285407 AAATATTTATTATTAAA
1 --ATATTTATTATTAAT
285424 ATATT
1 ATATT
285429 AATATTGAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
15 13 0.41
16 2 0.06
17 7 0.22
18 2 0.06
19 8 0.25
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (15 bp):
ATATTTATTATTAAT
Found at i:285492 original size:16 final size:16
Alignment explanation
Indices: 285461--285497 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
285451 ATGTGAAGAC
285461 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
285477 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
285493 TATTA
1 TATTA
285498 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:285530 original size:20 final size:21
Alignment explanation
Indices: 285505--285550 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
285495 TTAAAATAAA
*
285505 ATTAAAATATTAAATAAT-TT
1 ATTAAAATAATAAATAATATT
*
285525 ATTAAAATAATAAATTATATT
1 ATTAAAATAATAAATAATATT
285546 ATTAA
1 ATTAA
285551 TTTATTATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 16 0.70
21 7 0.30
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
ATTAAAATAATAAATAATATT
Found at i:287128 original size:19 final size:19
Alignment explanation
Indices: 287104--287141 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
287094 AAGTTAATAA
287104 CAAATTTGATTACAGTGGG
1 CAAATTTGATTACAGTGGG
287123 CAAATTTGATTACAGTGGG
1 CAAATTTGATTACAGTGGG
287142 TGGCAGTGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.26, T:0.32
Consensus pattern (19 bp):
CAAATTTGATTACAGTGGG
Found at i:288920 original size:4 final size:4
Alignment explanation
Indices: 288911--288938 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
288901 CAAATAAACG
288911 AGAA AGAA AGAA AGAA AGAA AGAA AGAA
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA
288939 GAAGAAGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:291566 original size:28 final size:28
Alignment explanation
Indices: 291535--291619 Score: 82
Period size: 28 Copynumber: 3.1 Consensus size: 28
291525 GATTTAATGT
*
291535 TTAGGGTTTTAAGTTTAGAATTTATGGG
1 TTAGGGTTTTAAGTTTAGAGTTTATGGG
* * * * ***
291563 TTAGAGTTTCAAGTATAGTGTTTATAAT
1 TTAGGGTTTTAAGTTTAGAGTTTATGGG
*
291591 TTAAGGTTTTAAGTTTAGAGTTTA-GGG
1 TTAGGGTTTTAAGTTTAGAGTTTATGGG
291618 TT
1 TT
291620 TAATGTTATG
Statistics
Matches: 41, Mismatches: 16, Indels: 1
0.71 0.28 0.02
Matches are distributed among these distances:
27 2 0.05
28 39 0.95
ACGTcount: A:0.27, C:0.01, G:0.25, T:0.47
Consensus pattern (28 bp):
TTAGGGTTTTAAGTTTAGAGTTTATGGG
Found at i:291613 original size:14 final size:14
Alignment explanation
Indices: 291527--291613 Score: 54
Period size: 14 Copynumber: 6.1 Consensus size: 14
291517 AGTTATAGGA
*
291527 TTTAATGTTTAGGGT
1 TTTAA-GTTTAGAGT
*
291542 TTTAAGTTTAGA-A
1 TTTAAGTTTAGAGT
* *
291555 TTTATGGGTTAGAGT
1 TTTA-AGTTTAGAGT
* * *
291570 TTCAAGTATAGTGT
1 TTTAAGTTTAGAGT
291584 TTATAA-TTTA-AGGT
1 TT-TAAGTTTAGA-GT
291598 TTTAAGTTTAGAGT
1 TTTAAGTTTAGAGT
291612 TT
1 TT
291614 AGGGTTTAAT
Statistics
Matches: 53, Mismatches: 13, Indels: 13
0.67 0.16 0.16
Matches are distributed among these distances:
13 7 0.13
14 35 0.66
15 11 0.21
ACGTcount: A:0.28, C:0.01, G:0.22, T:0.49
Consensus pattern (14 bp):
TTTAAGTTTAGAGT
Found at i:292010 original size:45 final size:45
Alignment explanation
Indices: 291879--292015 Score: 186
Period size: 45 Copynumber: 3.0 Consensus size: 45
291869 GGAAGGATTA
* * **
291879 GAGTATTGCGGTGGCTCGTCAAACTCA-ACTTGATATCCTTCCCTT
1 GAGTATTGCGGTGGCTCGTCAAACTGAGGC-TGATATCCTTGGCTT
* *
291924 GAGTATTGCGGTGGCTCGTCAAATTGAGGCTGATATTCTTGGCTT
1 GAGTATTGCGGTGGCTCGTCAAACTGAGGCTGATATCCTTGGCTT
* *
291969 GAGTATTGCGGTGACTCGTCAAACTGAGGCTGGTATCCTTGGCTT
1 GAGTATTGCGGTGGCTCGTCAAACTGAGGCTGATATCCTTGGCTT
292014 GA
1 GA
292016 TGAGCTATGC
Statistics
Matches: 81, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
45 80 0.99
46 1 0.01
ACGTcount: A:0.19, C:0.20, G:0.28, T:0.33
Consensus pattern (45 bp):
GAGTATTGCGGTGGCTCGTCAAACTGAGGCTGATATCCTTGGCTT
Found at i:293921 original size:16 final size:16
Alignment explanation
Indices: 293902--293950 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
293892 ATGATGAGAT
293902 ATTATTTTGATAATTA
1 ATTATTTTGATAATTA
*
293918 ATTATTTTTAT-ATT-
1 ATTATTTTGATAATTA
*
293932 A-TATTTTGGTAATTA
1 ATTATTTTGATAATTA
293947 ATTA
1 ATTA
293951 GCTAAGTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
13 7 0.26
14 4 0.15
15 4 0.15
16 12 0.44
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (16 bp):
ATTATTTTGATAATTA
Found at i:294456 original size:20 final size:21
Alignment explanation
Indices: 294428--294472 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
294418 TTTACTTACT
294428 ATTACTAAC-AACAAAATAAA
1 ATTACTAACTAACAAAATAAA
* * *
294448 ATTATTAACTAGCAAAATTAA
1 ATTACTAACTAACAAAATAAA
294469 ATTA
1 ATTA
294473 AAGTAAATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.58, C:0.11, G:0.02, T:0.29
Consensus pattern (21 bp):
ATTACTAACTAACAAAATAAA
Found at i:294573 original size:23 final size:23
Alignment explanation
Indices: 294547--294624 Score: 70
Period size: 23 Copynumber: 3.3 Consensus size: 23
294537 CTAGAACAAC
294547 ATTAAA-TAACAAATCAATTAAAA
1 ATTAAATTAACAAATCAA-TAAAA
*
294570 ATTAAATTAAACAAAACAA-AAAA
1 ATTAAATT-AACAAATCAATAAAA
* *
294593 CTTAAATTAATCAAATTAACTAACAA
1 ATTAAATTAA-CAAATCAA-TAA-AA
294619 ATTAAA
1 ATTAAA
294625 ATATTTTAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
22 2 0.05
23 23 0.52
24 1 0.02
25 11 0.25
26 7 0.16
ACGTcount: A:0.64, C:0.10, G:0.00, T:0.26
Consensus pattern (23 bp):
ATTAAATTAACAAATCAATAAAA
Found at i:294642 original size:12 final size:12
Alignment explanation
Indices: 294627--294651 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
294617 AAATTAAAAT
294627 ATTTTAAAATTA
1 ATTTTAAAATTA
294639 ATTTTAAAATTA
1 ATTTTAAAATTA
294651 A
1 A
294652 CCAAACTTCA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
ATTTTAAAATTA
Found at i:294843 original size:9 final size:9
Alignment explanation
Indices: 294826--294855 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
294816 TTTTTTTTTC
294826 CTTCTCCTT
1 CTTCTCCTT
*
294835 CTTCCCCTT
1 CTTCTCCTT
294844 CTTCTCCTT
1 CTTCTCCTT
294853 CTT
1 CTT
294856 TCTTTCTTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (9 bp):
CTTCTCCTT
Found at i:294866 original size:18 final size:18
Alignment explanation
Indices: 294822--294881 Score: 61
Period size: 17 Copynumber: 3.4 Consensus size: 18
294812 TACCTTTTTT
* *
294822 TTTCCTTCTCCTTCTTCCC
1 TTTCTTTCTCCTTCTT-TC
*
294841 CTTC-TTCTCCTTCTTTC
1 TTTCTTTCTCCTTCTTTC
*
294858 TTTCTTTCT-CTTTTTTC
1 TTTCTTTCTCCTTCTTTC
294875 TTTCTTT
1 TTTCTTT
294882 TTTCCTTCAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
17 18 0.50
18 15 0.42
19 3 0.08
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTCTTTCTCCTTCTTTC
Found at i:294874 original size:13 final size:13
Alignment explanation
Indices: 294852--294884 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
294842 TTCTTCTCCT
294852 TCTTTCTTTCTTTC
1 TCTTT-TTTCTTTC
294866 TCTTTTTTCTTTC
1 TCTTTTTTCTTTC
294879 T-TTTTT
1 TCTTTTT
294885 CCTTCAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 5 0.26
13 9 0.47
14 5 0.26
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (13 bp):
TCTTTTTTCTTTC
Found at i:298148 original size:15 final size:15
Alignment explanation
Indices: 298128--298192 Score: 78
Period size: 15 Copynumber: 4.2 Consensus size: 15
298118 ATATAATTAT
298128 TTTTATATTAAAATA
1 TTTTATATTAAAATA
*
298143 TTTTATTTTAAATTATA
1 TTTTATATTAAA--ATA
*
298160 TTTTGA-AATAAAATA
1 TTTT-ATATTAAAATA
298175 TTTTATATTAAAATA
1 TTTTATATTAAAATA
298190 TTT
1 TTT
298193 CAAATATTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
14 1 0.02
15 29 0.69
17 11 0.26
18 1 0.02
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (15 bp):
TTTTATATTAAAATA
Found at i:299634 original size:29 final size:28
Alignment explanation
Indices: 299583--299661 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 28
299573 CAAATAATTT
*
299583 TAAAATTATTAAAATTATTTTTTTAATATA
1 TAAAATTATT-AAATTA-TTTTTTAAAATA
*
299613 TAAAATGTTTTAAATTATTTTTTAAAATA
1 TAAAAT-TATTAAATTATTTTTTAAAATA
*
299642 TAAAATTATTAAATAATTTT
1 TAAAATTATTAAATTATTTT
299662 AGTTTTCAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
28 12 0.27
29 17 0.39
30 12 0.27
31 3 0.07
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (28 bp):
TAAAATTATTAAATTATTTTTTAAAATA
Found at i:300507 original size:11 final size:10
Alignment explanation
Indices: 300491--300590 Score: 54
Period size: 11 Copynumber: 10.1 Consensus size: 10
300481 GATGATGATT
300491 ATAATTTTAAA
1 ATAATTTT-AA
300502 ATAATTTT-A
1 ATAATTTTAA
*
300511 AT-ATTTT-T
1 ATAATTTTAA
300519 AT-ATTTTAAAAA
1 ATAATTTT---AA
300531 ATAATTTTAA
1 ATAATTTTAA
300541 ATTAATTTT-A
1 A-TAATTTTAA
300551 ATAATTTT--
1 ATAATTTTAA
300559 AT-ATTTTAA
1 ATAATTTTAA
* *
300568 AAAATACTTTTA
1 ATAAT--TTTAA
300580 ATAATTTTAA
1 ATAATTTTAA
300590 A
1 A
300591 ATCATTTGCT
Statistics
Matches: 72, Mismatches: 6, Indels: 23
0.71 0.06 0.23
Matches are distributed among these distances:
7 5 0.07
8 14 0.19
9 11 0.15
10 12 0.17
11 15 0.21
12 10 0.14
13 5 0.07
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (10 bp):
ATAATTTTAA
Found at i:300533 original size:20 final size:20
Alignment explanation
Indices: 300510--300591 Score: 69
Period size: 20 Copynumber: 4.0 Consensus size: 20
300500 AAATAATTTT
*
300510 AATATTTTTATATTTTAAAA
1 AATAATTTTATATTTTAAAA
* **
300530 AATAATTTTA-A-ATTAATTTT
1 AATAATTTTATATTTTAA--AA
300550 AATAATTTTATATTTTAAAA
1 AATAATTTTATATTTTAAAA
*
300570 AATACTTTTAATAATTTTAAAA
1 AATAATTTT-AT-ATTTTAAAA
300592 TCATTTGCTG
Statistics
Matches: 48, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
18 4 0.08
19 1 0.02
20 27 0.56
21 3 0.06
22 13 0.27
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (20 bp):
AATAATTTTATATTTTAAAA
Found at i:300547 original size:40 final size:39
Alignment explanation
Indices: 300491--300589 Score: 155
Period size: 40 Copynumber: 2.5 Consensus size: 39
300481 GATGATGATT
*
300491 ATAATTTTAAAATAATTTTAATATTTTTATATTTTAAAAA
1 ATAATTTT-AAATAATTTTAATAATTTTATATTTTAAAAA
300531 ATAATTTTAAATTAATTTTAATAATTTTATATTTTAAAAA
1 ATAATTTTAAA-TAATTTTAATAATTTTATATTTTAAAAA
*
300571 ATACTTTT-AATAATTTTAA
1 ATAATTTTAAATAATTTTAA
300590 AATCATTTGC
Statistics
Matches: 56, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
38 9 0.16
39 5 0.09
40 42 0.75
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (39 bp):
ATAATTTTAAATAATTTTAATAATTTTATATTTTAAAAA
Found at i:303295 original size:80 final size:80
Alignment explanation
Indices: 303153--303534 Score: 486
Period size: 80 Copynumber: 4.8 Consensus size: 80
303143 ACAATTATGA
* **
303153 CACCCAGTG-TCTAGCGGA-ATAACCCCGAAA-GTGAGCCCAGCTCTAGTTGGATT-AA-CGAAC
1 CACCCAGTGCT-TAGCGGATA-AACCGC-AAATGTGAGCCCAGCTCTAGTCAG-TTAAACCG-AC
* *
303213 AAATATTCGTCAAATCCTAG
61 AAATATCCGTCAAATCTTAG
* * *
303233 CACTCAGTGCTTAGCGGATAAACCGCAAATGTGAGCCCAGCTCTTGTCAGTTAAACAGACAAATA
1 CACCCAGTGCTTAGCGGATAAACCGCAAATGTGAGCCCAGCTCTAGTCAGTTAAACCGACAAATA
303298 TCCGTCAAATCTTAG
66 TCCGTCAAATCTTAG
* *
303313 TACCCAGTGCTTAGCGGATAAACCGCAAATGTGAGCCCAGCTCTAGTCAGTTAAACCGATAAATA
1 CACCCAGTGCTTAGCGGATAAACCGCAAATGTGAGCCCAGCTCTAGTCAGTTAAACCGACAAATA
303378 TCCGTCAAATCTTAG
66 TCCGTCAAATCTTAG
* * * **
303393 CACCCAGTGTTTAGTGGATAAACTGCAAATGTGAGCCCAGCTCTAGTTGGTTAAACCGACAAATA
1 CACCCAGTGCTTAGCGGATAAACCGCAAATGTGAGCCCAGCTCTAGTCAGTTAAACCGACAAATA
* *
303458 TCTGTCAAATCTTGG
66 TCCGTCAAATCTTAG
* * * * *
303473 CACCCAGTGCCTAGCAGATAAACCGCAATTGTGAGCCCAACTCTAGTCAGTTAAACTGACAA
1 CACCCAGTGCTTAGCGGATAAACCGCAAATGTGAGCCCAGCTCTAGTCAGTTAAACCGACAA
303535 CATGTATTCA
Statistics
Matches: 265, Mismatches: 32, Indels: 10
0.86 0.10 0.03
Matches are distributed among these distances:
79 5 0.02
80 257 0.97
81 3 0.01
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.23
Consensus pattern (80 bp):
CACCCAGTGCTTAGCGGATAAACCGCAAATGTGAGCCCAGCTCTAGTCAGTTAAACCGACAAATA
TCCGTCAAATCTTAG
Found at i:304253 original size:169 final size:167
Alignment explanation
Indices: 303976--304311 Score: 584
Period size: 169 Copynumber: 2.0 Consensus size: 167
303966 ATGATTCATT
* *
303976 CCATAATCATTTTTATATGTACACAATATATATATATACGATTAGATATCAATTTAATTAACAAC
1 CCATAATCATTTTTATATGTACACAATATATATATATACGATTAGATATAAAATTAATTAACAAC
304041 GTAACTAATTAAATAACTAAAGTTCGAGTTTCAAGAACTATGAACTTACCAAAAAGTTTAGGTTA
66 GTAACTAATTAAATAACTAAAGTTCGAGTTTCAAGAACTATGAACTTACCAAAAAGTTTAGGTTA
* *
304106 CTTTTCTGTTGATTGAGTCGATTATTCACCAACTTTC
131 CTTTTCCGTTGATTGAATCGATTATTCACCAACTTTC
304143 CCATAATCATTTTTATATAG-ACACAATATATATATATCTACGATTAGATATAAAATTAATTAAC
1 CCATAATCATTTTTATAT-GTACACAATATATATATA--TACGATTAGATATAAAATTAATTAAC
* *
304207 AACTTAACTAATTAAATAATTAAAGTTCGAGTTTCAAGAACTATGAACTTACCAAAAAGTTTAGG
63 AACGTAACTAATTAAATAACTAAAGTTCGAGTTTCAAGAACTATGAACTTACCAAAAAGTTTAGG
304272 TTACTTTTCCGTTGATTGAATCGATTATTCACCAACTTTC
128 TTACTTTTCCGTTGATTGAATCGATTATTCACCAACTTTC
304312 TCCTTCCCTC
Statistics
Matches: 160, Mismatches: 6, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
167 34 0.21
168 1 0.01
169 125 0.78
ACGTcount: A:0.39, C:0.15, G:0.10, T:0.37
Consensus pattern (167 bp):
CCATAATCATTTTTATATGTACACAATATATATATATACGATTAGATATAAAATTAATTAACAAC
GTAACTAATTAAATAACTAAAGTTCGAGTTTCAAGAACTATGAACTTACCAAAAAGTTTAGGTTA
CTTTTCCGTTGATTGAATCGATTATTCACCAACTTTC
Found at i:304523 original size:17 final size:16
Alignment explanation
Indices: 304484--304528 Score: 63
Period size: 17 Copynumber: 2.8 Consensus size: 16
304474 AGCCTATTGG
*
304484 AAATTGAATTTATTTA
1 AAATTAAATTTATTTA
*
304500 AATTTAAATTTATTATA
1 AAATTAAATTTATT-TA
304517 AAATTAAATTTA
1 AAATTAAATTTA
304529 GAAAGTCCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
16 12 0.48
17 13 0.52
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (16 bp):
AAATTAAATTTATTTA
Found at i:304588 original size:15 final size:15
Alignment explanation
Indices: 304568--304599 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
304558 GTACAGATCT
304568 AAATGGCCCAATTAC
1 AAATGGCCCAATTAC
304583 AAATGGCCCAATTAC
1 AAATGGCCCAATTAC
304598 AA
1 AA
304600 TCTTGGACCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.44, C:0.25, G:0.12, T:0.19
Consensus pattern (15 bp):
AAATGGCCCAATTAC
Found at i:305299 original size:12 final size:12
Alignment explanation
Indices: 305270--305315 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
305260 ACTTAATGTC
305270 AATAATAA-ATTT
1 AATAATAATA-TT
*
305282 ATTAATAATATT
1 AATAATAATATT
*
305294 AATAATAATAAT
1 AATAATAATATT
305306 AATAATAATA
1 AATAATAATA
305316 AATGTAACAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
12 29 0.97
13 1 0.03
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
AATAATAATATT
Found at i:305334 original size:3 final size:3
Alignment explanation
Indices: 305284--305316 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
305274 ATAAATTTAT
*
305284 TAA TAA TAT TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
305317 ATGTAACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:306519 original size:30 final size:29
Alignment explanation
Indices: 306426--306897 Score: 488
Period size: 29 Copynumber: 16.0 Consensus size: 29
306416 GAAGGTCCCT
* *
306426 AAACTGTCCGAAAATTCTATTTTTAGCCCC-
1 AAACT-TCCAAAAATTCCATTTTTA-CCCCG
* * *
306456 AAACTTCCAAAAATCCCATTTTGACCTCG
1 AAACTTCCAAAAATTCCATTTTTACCCCG
*
306485 AAACTTCCAAAAATTTCATTTTTACCCCCG
1 AAACTTCCAAAAATTCCATTTTTA-CCCCG
*
306515 AAACTTCCAAAAATTCTATTTTTACTCCCG
1 AAACTTCCAAAAATTCCATTTTTAC-CCCG
* * *
306545 -AACTTCCAAATATTCCGTTTTTACCCCCA
1 AAACTTCCAAAAATTCCATTTTTA-CCCCG
306574 AAACTTCCAAAAATTCCATTTTTACCTCC-
1 AAACTTCCAAAAATTCCATTTTTACC-CCG
* *
306603 AAACTTCCAAAAATCCCATTTTTGACCCCA
1 AAACTTCCAAAAATTCCATTTTT-ACCCCG
*
306633 AAACTTCCAAAAATTCCATTTTTACCCCT
1 AAACTTCCAAAAATTCCATTTTTACCCCG
* *
306662 AAACTTCCAGAAA-TCCTATTTTTGACCTCG
1 AAACTTCCAAAAATTCC-ATTTTT-ACCCCG
* *
306692 AAACTTCCAAAAATTTCATTTTTACCCCT
1 AAACTTCCAAAAATTCCATTTTTACCCCG
* *
306721 AAACTTCCAAAAATCCCATTTTTTGACCCCA
1 AAACTTCCAAAAATTCCA-TTTTT-ACCCCG
*
306752 AAACTTCCAAAAATTCCATTTTTACCCCC
1 AAACTTCCAAAAATTCCATTTTTACCCCG
* *
306781 AAACTTCCAAAAA-TCTCATTTTTTATCTCG
1 AAACTTCCAAAAATTC-CA-TTTTTACCCCG
*
306811 AAACTTCCAAAAATTCCGTTTTTACCCCCG
1 AAACTTCCAAAAATTCCATTTTTA-CCCCG
** * * *
306841 -AACTTCCAAAAACACCGTTTTTTATCCCA
1 AAACTTCCAAAAATTCC-ATTTTTACCCCG
* * *
306870 AAATTTCTAAAAATTCTATTTTTACCCC
1 AAACTTCCAAAAATTCCATTTTTACCCC
306898 CGAATGTCTA
Statistics
Matches: 373, Mismatches: 50, Indels: 39
0.81 0.11 0.08
Matches are distributed among these distances:
28 8 0.02
29 181 0.49
30 158 0.42
31 26 0.07
ACGTcount: A:0.33, C:0.30, G:0.04, T:0.33
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTACCCCG
Found at i:306901 original size:59 final size:59
Alignment explanation
Indices: 306445--306898 Score: 529
Period size: 59 Copynumber: 7.7 Consensus size: 59
306435 GAAAATTCTA
* * * * **
306445 TTTTTAGCCCC-AAACTTCCAAAAATCCCATTTTGACCTCGAAACTTCCAAAAATTTCA-
1 TTTTTA-CCCCAAAACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATCCCAT
* * * * * * *
306503 TTTTTACCCCCGAAACTTCCAAAAATTCTATTTTTACTCCCGAACTTCCAAATATTCC-G
1 TTTTTA-CCCCAAAACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATCCCAT
*
306562 TTTTTACCCCCAAAACTTCCAAAAATTCCATTTTTACCTCCAAACTTCCAAAAATCCCAT
1 TTTTTA-CCCCAAAACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATCCCAT
* * * *
306622 TTTTGACCCCAAAACTTCCAAAAATTCCATTTTTACCCCTAAACTTCCAGAAATCCTAT
1 TTTTTACCCCAAAACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATCCCAT
* * * * *
306681 TTTTGACCTCGAAACTTCCAAAAATTTCATTTTTACCCCTAAACTTCCAAAAATCCCAT
1 TTTTTACCCCAAAACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATCCCAT
*
306740 TTTTTGACCCCAAAACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATCTCAT
1 TTTTT-ACCCCAAAACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATCCCAT
* * * * * *
306800 TTTTTATCTCGAAACTTCCAAAAATTCCGTTTTTACCCCCGAACTTCCAAAAA-CACCGT
1 TTTTTACCCCAAAACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATC-CCAT
* * * *
306859 TTTTTATCCCAAAATTTCTAAAAATTCTATTTTTACCCCC
1 TTTTTACCCCAAAACTTCCAAAAATTCCATTTTTACCCCC
306899 GAATGTCTAA
Statistics
Matches: 344, Mismatches: 47, Indels: 9
0.86 0.12 0.02
Matches are distributed among these distances:
58 11 0.03
59 274 0.80
60 59 0.17
ACGTcount: A:0.33, C:0.30, G:0.03, T:0.34
Consensus pattern (59 bp):
TTTTTACCCCAAAACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATCCCAT
Found at i:307332 original size:96 final size:95
Alignment explanation
Indices: 307190--307381 Score: 244
Period size: 96 Copynumber: 2.0 Consensus size: 95
307180 GAAACTTTAA
* * **
307190 AATCGAGGCAATATTCTTTTATTTCGAGTTTCGAAAATTTGTGCCTTAACTCACTAGGTGCAATT
1 AATCGAGGCAATATTCTTTTATTTCGAG-TTCGAAAATTTGCGCCTTAACTCACTAGGCGCAACC
307255 TTTCCTCAAATCGAAATAATCGAATACCCTT
65 TTTCCTCAAATCGAAATAATCGAATACCCTT
* * *
307286 AATCGAGGCAATGTT-TTCTTATCTTCGA-TTCTAAAATATTGCGCCTTAACTTACTAGGCGCAA
1 AATCGAGGCAATATTCTT-TTAT-TTCGAGTTCGAAAAT-TTGCGCCTTAACTCACTAGGCGCAA
* * *
307349 CCTTTCTTCAAATCGAGATAATCGAATATCCTT
63 CCTTTCCTCAAATCGAAATAATCGAATACCCTT
307382 TTCCCAAAAA
Statistics
Matches: 83, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
95 10 0.12
96 68 0.82
97 5 0.06
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.36
Consensus pattern (95 bp):
AATCGAGGCAATATTCTTTTATTTCGAGTTCGAAAATTTGCGCCTTAACTCACTAGGCGCAACCT
TTCCTCAAATCGAAATAATCGAATACCCTT
Found at i:308604 original size:19 final size:18
Alignment explanation
Indices: 308582--308643 Score: 61
Period size: 19 Copynumber: 3.1 Consensus size: 18
308572 AACAAAATAT
308582 TTCAAAATAATTTTTAAAA
1 TTCAAAAT-ATTTTTAAAA
*
308601 TTCAAAATATTTATAAAAA
1 TTCAAAATATTT-TTAAAA
308620 TTCTAAAATTTATATTTTAAAA
1 TTC-AAAA--TAT-TTTTAAAA
308642 TT
1 TT
308644 TTTTTTAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
18 4 0.11
19 16 0.44
20 4 0.11
22 10 0.28
23 2 0.06
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (18 bp):
TTCAAAATATTTTTAAAA
Found at i:323060 original size:6 final size:6
Alignment explanation
Indices: 323051--323099 Score: 80
Period size: 6 Copynumber: 7.8 Consensus size: 6
323041 GTAGGATGGA
323051 TGGCAG TGGCAG TGGCAG TGGCAG TGGCAG TGGCAAG TGGCAAG TGGCA
1 TGGCAG TGGCAG TGGCAG TGGCAG TGGCAG TGGC-AG TGGC-AG TGGCA
323100 TTTTATAGTA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
6 29 0.69
7 13 0.31
ACGTcount: A:0.20, C:0.16, G:0.47, T:0.16
Consensus pattern (6 bp):
TGGCAG
Found at i:323588 original size:2 final size:2
Alignment explanation
Indices: 323581--323618 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
323571 AGGACATGAT
323581 TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
323619 TTGATTCCCA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:324254 original size:2 final size:2
Alignment explanation
Indices: 324237--324292 Score: 94
Period size: 2 Copynumber: 27.0 Consensus size: 2
324227 CAAAAATAAA
324237 AT AT CAT AT CAT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT -AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
324281 AT AT AT AT AT AT
1 AT AT AT AT AT AT
324293 TACAAGGTAG
Statistics
Matches: 52, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
2 48 0.92
3 4 0.08
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:327400 original size:14 final size:14
Alignment explanation
Indices: 327383--327443 Score: 52
Period size: 14 Copynumber: 4.2 Consensus size: 14
327373 GTTTAATTAA
327383 AATTAATTAACTTT
1 AATTAATTAACTTT
* *
327397 AATTAATCAAAATTT
1 AATTAAT-TAACTTT
* *
327412 AAACTAATTAA-TAAT
1 -AATTAATTAACT-TT
327427 AATTAATTAACTTT
1 AATTAATTAACTTT
327441 AAT
1 AAT
327444 CAAATTTAAC
Statistics
Matches: 36, Mismatches: 7, Indels: 8
0.71 0.14 0.16
Matches are distributed among these distances:
14 21 0.58
15 9 0.25
16 6 0.17
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
AATTAATTAACTTT
Found at i:327442 original size:20 final size:21
Alignment explanation
Indices: 327374--327443 Score: 67
Period size: 20 Copynumber: 3.3 Consensus size: 21
327364 TCTTTTATAG
327374 TTTAATTAA-AATTAATTAAC
1 TTTAATTAATAATTAATTAAC
327394 TTTAATTAATCAA--AATTTAAAC
1 TTTAATTAAT-AATTAA-TT-AAC
327416 TAATTAA-TAATAATTAATTAAC
1 T--TTAATTAATAATTAATTAAC
327438 TTTAAT
1 TTTAAT
327444 CAAATTTAAC
Statistics
Matches: 41, Mismatches: 0, Indels: 17
0.71 0.00 0.29
Matches are distributed among these distances:
20 15 0.37
21 2 0.05
22 12 0.29
23 6 0.15
24 6 0.15
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (21 bp):
TTTAATTAATAATTAATTAAC
Done.