Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr13
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: 91551117
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2824764 characters in sequence are not A, C, G, or T
File 79 of 276
Found at i:24238086 original size:25 final size:26
Alignment explanation
Indices: 24238058--24238110 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 26
24238048 TACGATGACT
24238058 ATGTAAAAAATT-TTAATAAA-TAAAA
1 ATGTAAAAAATTATTAA-AAATTAAAA
**
24238083 ATGTTTAAAATTATTAAAAATTAAAA
1 ATGTAAAAAATTATTAAAAATTAAAA
24238109 AT
1 AT
24238111 AATATAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 13 0.54
26 11 0.46
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (26 bp):
ATGTAAAAAATTATTAAAAATTAAAA
Found at i:24238949 original size:22 final size:21
Alignment explanation
Indices: 24238907--24238971 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 21
24238897 ACTTCATGGT
*
24238907 AATTTTTTGAATTTTTATAAAAA
1 AATTTTTT-TATTTTT-TAAAAA
24238930 AATTTGTTTTATTTTTT-AAAA
1 AATTT-TTTTATTTTTTAAAAA
* *
24238951 TATTTTTTTATAATTTTAAAA
1 AATTTTTTTAT-TTTTTAAAA
24238972 TTGTTTCTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
20 6 0.17
21 12 0.33
22 4 0.11
23 11 0.31
24 3 0.08
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.58
Consensus pattern (21 bp):
AATTTTTTTATTTTTTAAAAA
Found at i:24243128 original size:19 final size:19
Alignment explanation
Indices: 24243083--24243132 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
24243073 AATCGAGACA
*
24243083 AAATTTTAAATATTAAATT
1 AAATATTAAATATTAAATT
24243102 -AATCATTAAA-ATTAAATTT
1 AAAT-ATTAAATATTAAA-TT
24243121 AAATATTAAATA
1 AAATATTAAATA
24243133 GTATGTTAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
18 9 0.35
19 13 0.50
20 4 0.15
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (19 bp):
AAATATTAAATATTAAATT
Found at i:24254468 original size:7 final size:7
Alignment explanation
Indices: 24254456--24254482 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
24254446 ATGATATTTT
24254456 TATTTAA
1 TATTTAA
24254463 TATTTAA
1 TATTTAA
24254470 TATTTAA
1 TATTTAA
24254477 TATTTA
1 TATTTA
24254483 GTAAATTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
TATTTAA
Found at i:24256024 original size:27 final size:26
Alignment explanation
Indices: 24255986--24256037 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
24255976 AGCCTTTTCT
*
24255986 GAAAGACTAA-TTGGATATAGAAATCG
1 GAAAGACTAATTTGAATATA-AAATCG
24256012 GAAAGATCTAATTTGAATATAAAATC
1 GAAAGA-CTAATTTGAATATAAAATC
24256038 ATACGAACTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 6 0.26
27 9 0.39
28 8 0.35
ACGTcount: A:0.48, C:0.08, G:0.17, T:0.27
Consensus pattern (26 bp):
GAAAGACTAATTTGAATATAAAATCG
Found at i:24256448 original size:11 final size:11
Alignment explanation
Indices: 24256434--24256460 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
24256424 TTTGTTGTCA
24256434 TTTTATTATTG
1 TTTTATTATTG
24256445 TTTTATTATTG
1 TTTTATTATTG
24256456 TTTTA
1 TTTTA
24256461 CTATCATTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.19, C:0.00, G:0.07, T:0.74
Consensus pattern (11 bp):
TTTTATTATTG
Found at i:24256459 original size:22 final size:22
Alignment explanation
Indices: 24256433--24256501 Score: 59
Period size: 22 Copynumber: 3.1 Consensus size: 22
24256423 TTTTGTTGTC
* *
24256433 ATTTTATTATTGTTTTATTATT
1 ATTTTATTATTATTTGATTATT
* * *
24256455 GTTTTACTATCATTTGATTATT
1 ATTTTATTATTATTTGATTATT
* *
24256477 ATATTATTATTAATTT-ATTGTT
1 ATTTTATTATT-ATTTGATTATT
24256499 ATT
1 ATT
24256502 GTTTGAATAT
Statistics
Matches: 35, Mismatches: 11, Indels: 2
0.73 0.23 0.04
Matches are distributed among these distances:
22 31 0.89
23 4 0.11
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (22 bp):
ATTTTATTATTATTTGATTATT
Found at i:24257075 original size:30 final size:30
Alignment explanation
Indices: 24257018--24257084 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
24257008 ATATTGGGTA
* ***
24257018 TATATTATTTAAGTAATAAATTGTTTATTT
1 TATATTATTTAAGTAAAAAAACATTTATTT
24257048 TATATTATTTAAGTAAAAAAACATTTATTT
1 TATATTATTTAAGTAAAAAAACATTTATTT
24257078 TAATATT
1 T-ATATT
24257085 CTAGTAATGA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 27 0.84
31 5 0.16
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.52
Consensus pattern (30 bp):
TATATTATTTAAGTAAAAAAACATTTATTT
Found at i:24272348 original size:25 final size:25
Alignment explanation
Indices: 24272320--24272377 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
24272310 TTAAAAAATA
*
24272320 AATATAT-TAATTTATTTTTATAT-T
1 AATATATATAA-TTATTTATATATGT
*
24272344 GAATAAATATAATTATTTATATATGT
1 -AATATATATAATTATTTATATATGT
24272370 AATATATA
1 AATATATA
24272378 AATATAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
25 24 0.86
26 4 0.14
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (25 bp):
AATATATATAATTATTTATATATGT
Found at i:24274987 original size:6 final size:6
Alignment explanation
Indices: 24274976--24275008 Score: 57
Period size: 6 Copynumber: 5.3 Consensus size: 6
24274966 TATCCTCTCC
24274976 TCTTTT TCTTTT TCTTTT TCTTTCT TCTTTT TC
1 TCTTTT TCTTTT TCTTTT TCTTT-T TCTTTT TC
24275009 CCTCACCAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 20 0.77
7 6 0.23
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (6 bp):
TCTTTT
Found at i:24276058 original size:20 final size:19
Alignment explanation
Indices: 24276022--24276061 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
24276012 CTCCTTGATT
**
24276022 ATTTAACTAACTGTGGTTA
1 ATTTAACTAACCATGGTTA
24276041 ATTTAACTTAACCATGGTTA
1 ATTTAAC-TAACCATGGTTA
24276061 A
1 A
24276062 ATTCCCTCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.40
Consensus pattern (19 bp):
ATTTAACTAACCATGGTTA
Found at i:24278944 original size:137 final size:139
Alignment explanation
Indices: 24278755--24279036 Score: 372
Period size: 137 Copynumber: 2.0 Consensus size: 139
24278745 GCCGTTTGTC
* *
24278755 AAATAATTCCTTCAATTTTGATGTTCTTTTTTTCTCAGGCGCGTAAAAATTATTAGGTTGGATTA
1 AAATAATTCCTTCAATTTTGAAGTTCTTTCTTTCTCAGGCGCGTAAAAATTATTAGGTTGGATTA
** * * * * *
24278820 TATTAACTTGTGGTGTT-AGAATTT-TTTTTAAAATATCATAATTAAATTATATATTTTTACGAT
66 TATTAAAATGTGGAGTTAAAAATTTCTTTTAAAAAGATCAGAATTAAATTATATATTTTTACGAT
*
24278883 GGTAAAAAT
131 AGTAAAAAT
* * * * *
24278892 AAATAATTCTTTTAATTTTTAAGTTC-TTCTTTCTGAGGCGTGTAAAATATTATTAGGTTGGATT
1 AAATAATTCCTTCAATTTTGAAGTTCTTTCTTTCTCAGGCGCGTAAAA-ATTATTAGGTTGGATT
* *
24278956 ATATTAAAATGTGGAGTTAAAAATTTCTTTTAAAAAGATCGGAATTAAATTATATATTTTTGCGA
65 ATATTAAAATGTGGAGTTAAAAATTTCTTTTAAAAAGATCAGAATTAAATTATATATTTTTACGA
24279021 TAGTAAAAAT
130 TAGTAAAAAT
24279031 ATAATA
1 A-AATA
24279037 TTATCATTTT
Statistics
Matches: 124, Mismatches: 17, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
136 18 0.15
137 53 0.43
138 6 0.05
139 43 0.35
140 4 0.03
ACGTcount: A:0.35, C:0.07, G:0.13, T:0.44
Consensus pattern (139 bp):
AAATAATTCCTTCAATTTTGAAGTTCTTTCTTTCTCAGGCGCGTAAAAATTATTAGGTTGGATTA
TATTAAAATGTGGAGTTAAAAATTTCTTTTAAAAAGATCAGAATTAAATTATATATTTTTACGAT
AGTAAAAAT
Found at i:24279066 original size:15 final size:16
Alignment explanation
Indices: 24279030--24279070 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
24279020 ATAGTAAAAA
24279030 TATAATATTATCATTTT
1 TATAAT-TTATCATTTT
*
24279047 AATAATTTAT-ATTTT
1 TATAATTTATCATTTT
24279062 TATAATTTA
1 TATAATTTA
24279071 GAGATTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 13 0.59
16 4 0.18
17 5 0.23
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (16 bp):
TATAATTTATCATTTT
Found at i:24280248 original size:9 final size:9
Alignment explanation
Indices: 24280234--24280382 Score: 50
Period size: 10 Copynumber: 15.0 Consensus size: 9
24280224 TATAAACAAT
24280234 TAAAAATTA
1 TAAAAATTA
*
24280243 TAAAAAATAA
1 T-AAAAATTA
* *
24280253 TTAGAACTTA
1 -TAAAAATTA
*
24280263 TAAATATTA
1 TAAAAATTA
24280272 TAATAAACTTA
1 TAA-AAA-TTA
*
24280283 -ATAAATT-
1 TAAAAATTA
24280290 TATAAAATTAA
1 TA-AAAATT-A
*
24280301 TAAAAACATATT
1 T-AAAA-AT-TA
*
24280313 TAAAATTTTA
1 TAAAA-ATTA
24280323 TAAAAATATA
1 TAAAAAT-TA
* *
24280333 TTAAAATTCT
1 TAAAAATT-A
24280343 TAAAAACTTA
1 TAAAAA-TTA
*
24280353 TAAAAATGA
1 TAAAAATTA
24280362 TAAAAAATTAA
1 T-AAAAATT-A
24280373 TAAAATATTA
1 TAAAA-ATTA
24280383 AAATTTATAT
Statistics
Matches: 102, Mismatches: 21, Indels: 33
0.65 0.13 0.21
Matches are distributed among these distances:
8 3 0.03
9 23 0.23
10 51 0.50
11 20 0.20
12 4 0.04
13 1 0.01
ACGTcount: A:0.60, C:0.03, G:0.01, T:0.36
Consensus pattern (9 bp):
TAAAAATTA
Found at i:24280280 original size:20 final size:20
Alignment explanation
Indices: 24280257--24280294 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
24280247 AAATAATTAG
24280257 AACTT-ATAAATATTATAATA
1 AACTTAATAAAT-TTATAATA
24280277 AACTTAATAAATTTATAA
1 AACTTAATAAATTTATAA
24280295 AATTAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.39
Consensus pattern (20 bp):
AACTTAATAAATTTATAATA
Found at i:24280316 original size:29 final size:27
Alignment explanation
Indices: 24280236--24280332 Score: 79
Period size: 29 Copynumber: 3.3 Consensus size: 27
24280226 TAAACAATTA
*
24280236 AAAATTATAAAAA-ATAATTAGAACTTAT
1 AAAATTATAAAAACAT-ATTA-AATTTAT
* *
24280264 AAATATTATAATAAACTTAATAAATTTAT
1 AAA-ATTATAA-AAACATATTAAATTTAT
24280293 AAAATTAATAAAAACATATTTAAAATTTTAT
1 AAAATT-ATAAAAACATA-TT-AAA-TTTAT
*
24280324 AAAAATATA
1 AAAATTATA
24280333 TTAAAATTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
28 12 0.21
29 21 0.38
30 12 0.21
31 11 0.20
ACGTcount: A:0.60, C:0.03, G:0.01, T:0.36
Consensus pattern (27 bp):
AAAATTATAAAAACATATTAAATTTAT
Found at i:24280328 original size:22 final size:21
Alignment explanation
Indices: 24280292--24280359 Score: 68
Period size: 20 Copynumber: 3.3 Consensus size: 21
24280282 AATAAATTTA
*
24280292 TAAAA-TTAATAAAAACATATT
1 TAAAATTTTATAAAAACATA-T
*
24280313 TAAAATTTTATAAAAATATAT
1 TAAAATTTTATAAAAACATAT
* *
24280334 TAAAATTCT-TAAAAACTTAT
1 TAAAATTTTATAAAAACATAT
*
24280354 AAAAAT
1 TAAAAT
24280360 GATAAAAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
20 14 0.35
21 14 0.35
22 12 0.30
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (21 bp):
TAAAATTTTATAAAAACATAT
Found at i:24280377 original size:30 final size:30
Alignment explanation
Indices: 24280234--24280377 Score: 93
Period size: 30 Copynumber: 4.8 Consensus size: 30
24280224 TATAAACAAT
* *
24280234 TAAAAATTATAAAAAA-TAATTAGAACTTA
1 TAAAAATTATAAAAAATTAATAAAAACTTA
* * *
24280263 TAAATATTATAATAAACTTAAT--AAATTTA
1 TAAAAATTATAA-AAAATTAATAAAAACTTA
* **
24280292 T-AAAATTAATAAAAACA-TATTTAAAATTTTA
1 TAAAAATT-ATAAAAA-ATTA-ATAAAAACTTA
* **
24280323 TAAAAA-TATATTAAAATTCTTAAAAACTTA
1 TAAAAATTATA-AAAAATTAATAAAAACTTA
*
24280353 TAAAAATGATAAAAAATTAATAAAA
1 TAAAAATTATAAAAAATTAATAAAA
24280378 TATTAAAATT
Statistics
Matches: 88, Mismatches: 16, Indels: 21
0.70 0.13 0.17
Matches are distributed among these distances:
28 10 0.11
29 22 0.25
30 33 0.38
31 19 0.22
32 4 0.05
ACGTcount: A:0.60, C:0.03, G:0.01, T:0.35
Consensus pattern (30 bp):
TAAAAATTATAAAAAATTAATAAAAACTTA
Found at i:24280394 original size:19 final size:20
Alignment explanation
Indices: 24280343--24280395 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 20
24280333 TTAAAATTCT
*
24280343 TAAAAACTTATA-AAAATGA
1 TAAAAAATTATATAAAATGA
24280362 TAAAAAATTA-ATAAAAT-A
1 TAAAAAATTATATAAAATGA
* *
24280380 TTAAAATTTATATAAA
1 TAAAAAATTATATAAA
24280396 TTTATTAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 10 0.34
19 19 0.66
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (20 bp):
TAAAAAATTATATAAAATGA
Found at i:24281594 original size:40 final size:40
Alignment explanation
Indices: 24281545--24281625 Score: 144
Period size: 40 Copynumber: 2.0 Consensus size: 40
24281535 TCATTATAGC
*
24281545 ATATATATGATTTTTTACCTATTAATAATTAATTTTATAT
1 ATATATATGATTTTTTACCTATTAAAAATTAATTTTATAT
*
24281585 ATATATATGATTTTTTACCTATTAAAAATTCATTTTATAT
1 ATATATATGATTTTTTACCTATTAAAAATTAATTTTATAT
24281625 A
1 A
24281626 GAATTTGACA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.53
Consensus pattern (40 bp):
ATATATATGATTTTTTACCTATTAAAAATTAATTTTATAT
Found at i:24285320 original size:194 final size:199
Alignment explanation
Indices: 24285108--24285502 Score: 586
Period size: 194 Copynumber: 2.0 Consensus size: 199
24285098 ACCATGAATT
* * *
24285108 ATATATGTACAAATATATATAAAAACATTTAAACGAAATATTATATAAAATGTTAAAATAATATG
1 ATATATGTACAAATATATATAAAAACATTAAAACCAAATATTATACAAAATGTTAAAATAATATG
* *** * * *
24285173 ATATAAAAAATAACTTCAAAATAATGAT-TTTATAAAAATAAAGTAAAATTATTAAAAATAGTTC
66 ATATAAAAAAGAACTTCAAAATAATGATACAAATAAAAACAAAGCAAAATTATT-AAAATAGCTC
* *
24285237 AACAC-ATATAAAAAATATTAAGTGAATT-T-TAA-AGTAA-TATACAAATAGAAAACTCAATCA
130 AACACAATATAAAAAATATTAAATGAATTCTAAAATAGTAAGTATACAAATAGAAAACTCAATCA
24285297 AAATA
195 AAATA
*
24285302 ATATATGTACAAATATATATAAAAATATTAAAACCAAATATTATACAAAATGTTAAAATAATATG
1 ATATATGTACAAATATATATAAAAACATTAAAACCAAATATTATACAAAATGTTAAAATAATATG
*
24285367 ATATAAAAAAGAACTTCAAAATAATTATACAAATAAAAACAAAGCAAAATTATTAAAATAGCTCA
66 ATATAAAAAAGAACTTCAAAATAATGATACAAATAAAAACAAAGCAAAATTATTAAAATAGCTCA
*
24285432 ACACATATATAAAAAATATTAAATGAATTCTAAAATAGTAAGTTATACAAATAGAAAACTCAATT
131 ACACA-ATATAAAAAATATTAAATGAATTCTAAAATAGTAAG-TATACAAATAGAAAACTCAATC
24285497 AAAATA
194 AAAATA
24285503 GAGCTAAAAT
Statistics
Matches: 178, Mismatches: 15, Indels: 9
0.88 0.07 0.04
Matches are distributed among these distances:
194 101 0.57
195 20 0.11
196 22 0.12
197 1 0.01
198 2 0.01
199 5 0.03
201 27 0.15
ACGTcount: A:0.58, C:0.07, G:0.05, T:0.29
Consensus pattern (199 bp):
ATATATGTACAAATATATATAAAAACATTAAAACCAAATATTATACAAAATGTTAAAATAATATG
ATATAAAAAAGAACTTCAAAATAATGATACAAATAAAAACAAAGCAAAATTATTAAAATAGCTCA
ACACAATATAAAAAATATTAAATGAATTCTAAAATAGTAAGTATACAAATAGAAAACTCAATCAA
AATA
Found at i:24285341 original size:25 final size:24
Alignment explanation
Indices: 24285310--24285375 Score: 73
Period size: 25 Copynumber: 2.7 Consensus size: 24
24285300 TAATATATGT
24285310 ACAAATATATATAAAAATATTAAA
1 ACAAATATATATAAAAATATTAAA
*
24285334 ACCAAATAT-TATACAAAATGTTAAA
1 A-CAAATATATATA-AAAATATTAAA
*
24285359 A-TAATATGATATAAAAA
1 ACAAATAT-ATATAAAAA
24285376 AGAACTTCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
23 5 0.14
24 9 0.25
25 22 0.61
ACGTcount: A:0.62, C:0.06, G:0.03, T:0.29
Consensus pattern (24 bp):
ACAAATATATATAAAAATATTAAA
Found at i:24285987 original size:16 final size:16
Alignment explanation
Indices: 24285966--24286020 Score: 83
Period size: 16 Copynumber: 3.4 Consensus size: 16
24285956 GTTTGGTTCA
*
24285966 CTGTAATGGAATAGGG
1 CTGTAATGGAATAGAG
*
24285982 CTGTAATTGAATAGAG
1 CTGTAATGGAATAGAG
*
24285998 TTGTAATGGAATAGAG
1 CTGTAATGGAATAGAG
24286014 CTGTAAT
1 CTGTAAT
24286021 CAGTAATTCA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.35, C:0.05, G:0.29, T:0.31
Consensus pattern (16 bp):
CTGTAATGGAATAGAG
Found at i:24286262 original size:15 final size:15
Alignment explanation
Indices: 24286228--24286272 Score: 63
Period size: 15 Copynumber: 2.9 Consensus size: 15
24286218 TCATATTTTA
* *
24286228 ATATAATTATTATTAT
1 ATATAATT-TAATAAT
24286244 ATATAATTTAATAAT
1 ATATAATTTAATAAT
24286259 ATATAATTTAATAA
1 ATATAATTTAATAA
24286273 CATTTTTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
15 19 0.70
16 8 0.30
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
ATATAATTTAATAAT
Found at i:24288000 original size:94 final size:94
Alignment explanation
Indices: 24287838--24288023 Score: 318
Period size: 94 Copynumber: 2.0 Consensus size: 94
24287828 GCCTATTACA
* *
24287838 AACACGTTGATGGAACTAAAGTCTTGATTTGTAATAAATGGGCTTATTGTACTCCACTCTTATAC
1 AACACGTTGATGGAACTAAAGTCTTGACTTGTAATAAATGGGCTTATTGTACTCCACTCCTATAC
*
24287903 ATAGATAATAGAATAATTTTTGACTAAGT
66 ATAGATAATAGAATAATTTTTAACTAAGT
* * *
24287932 AACACGTTGATGGAACTAAAGTCTTGACTTGTAATAAATGGGCTTCTTTTACTCCACTCCTATTC
1 AACACGTTGATGGAACTAAAGTCTTGACTTGTAATAAATGGGCTTATTGTACTCCACTCCTATAC
24287997 ATAGATAATAGAATAATTTTTAACTAA
66 ATAGATAATAGAATAATTTTTAACTAA
24288024 ATACGCATAA
Statistics
Matches: 86, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
94 86 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.36
Consensus pattern (94 bp):
AACACGTTGATGGAACTAAAGTCTTGACTTGTAATAAATGGGCTTATTGTACTCCACTCCTATAC
ATAGATAATAGAATAATTTTTAACTAAGT
Found at i:24288682 original size:14 final size:14
Alignment explanation
Indices: 24288665--24288693 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
24288655 AAATAATACT
24288665 TTTCAAATATGTAA
1 TTTCAAATATGTAA
24288679 TTTCAAATATGTAA
1 TTTCAAATATGTAA
24288693 T
1 T
24288694 GCAGTTTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (14 bp):
TTTCAAATATGTAA
Found at i:24288922 original size:85 final size:85
Alignment explanation
Indices: 24288779--24288950 Score: 299
Period size: 85 Copynumber: 2.0 Consensus size: 85
24288769 CGATAACATT
* * * *
24288779 TTTATAATTTTATTATCAATTAGTAGTAACTCGAGGCTCTCACTCTGGCCAAAATCACTCTGCAG
1 TTTATAATTTTATGATAAATTAGTAGTAACTCGAGCCTCTCACTCTGGCCAAAATCACTCTGCAA
24288844 CACCGCGAGTGATTCCAAGC
66 CACCGCGAGTGATTCCAAGC
*
24288864 TTTATAATTTTATGATAAATTAGTAGTAACTCGAGCCTCTCACTCTGGCCAAAATCACTTTGCAA
1 TTTATAATTTTATGATAAATTAGTAGTAACTCGAGCCTCTCACTCTGGCCAAAATCACTCTGCAA
24288929 CACCGCGAGTGATTCCAAGC
66 CACCGCGAGTGATTCCAAGC
24288949 TT
1 TT
24288951 CCAACCACGA
Statistics
Matches: 82, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
85 82 1.00
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (85 bp):
TTTATAATTTTATGATAAATTAGTAGTAACTCGAGCCTCTCACTCTGGCCAAAATCACTCTGCAA
CACCGCGAGTGATTCCAAGC
Found at i:24292554 original size:27 final size:26
Alignment explanation
Indices: 24292522--24292580 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
24292512 GATTGAAATG
*
24292522 TTATTTGATAAATTAAAAGATTATGTA
1 TTATTTGATAAA-TAAAAGATTATATA
* * * *
24292549 TTATTTTATGAATAAAATATTTTATA
1 TTATTTGATAAATAAAAGATTATATA
24292575 TTATTT
1 TTATTT
24292581 TAAATATTTC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 17 0.63
27 10 0.37
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.53
Consensus pattern (26 bp):
TTATTTGATAAATAAAAGATTATATA
Found at i:24301154 original size:31 final size:31
Alignment explanation
Indices: 24301095--24301154 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
24301085 AAGAAATCTA
* *
24301095 TATAGGGACTAAAATTGAATAAATTAAAAAG
1 TATAGAGACTAAAATTGAATAAAATAAAAAG
*
24301126 TATAGAGATTAAAATTG-ATCAAAATAAAA
1 TATAGAGACTAAAATTGAAT-AAAATAAAA
24301155 TAAAAAATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 2 0.08
31 23 0.92
ACGTcount: A:0.57, C:0.03, G:0.13, T:0.27
Consensus pattern (31 bp):
TATAGAGACTAAAATTGAATAAAATAAAAAG
Found at i:24312571 original size:33 final size:33
Alignment explanation
Indices: 24312527--24312613 Score: 165
Period size: 33 Copynumber: 2.6 Consensus size: 33
24312517 ATACGTTTCG
24312527 CACTGTCTGAGCGGAGACTATTACTTTGCTTAC
1 CACTGTCTGAGCGGAGACTATTACTTTGCTTAC
*
24312560 CGCTGTCTGAGCGGAGACTATTACTTTGCTTAC
1 CACTGTCTGAGCGGAGACTATTACTTTGCTTAC
24312593 CACTGTCTGAGCGGAGACTAT
1 CACTGTCTGAGCGGAGACTAT
24312614 CTCCTTTAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 52 1.00
ACGTcount: A:0.21, C:0.24, G:0.24, T:0.31
Consensus pattern (33 bp):
CACTGTCTGAGCGGAGACTATTACTTTGCTTAC
Found at i:24313296 original size:29 final size:24
Alignment explanation
Indices: 24313244--24313292 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
24313234 GAAGGTAGGA
24313244 AGCCAAAAATAAAATAAATGAACT
1 AGCCAAAAATAAAATAAATGAACT
24313268 AGCCAAAAATAAAATAAATGAACT
1 AGCCAAAAATAAAATAAATGAACT
24313292 A
1 A
24313293 AACTGAACTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.63, C:0.12, G:0.08, T:0.16
Consensus pattern (24 bp):
AGCCAAAAATAAAATAAATGAACT
Found at i:24314504 original size:29 final size:28
Alignment explanation
Indices: 24314471--24314563 Score: 69
Period size: 29 Copynumber: 3.1 Consensus size: 28
24314461 AAAAAGTTGG
24314471 TCCTTATTTGACTACTTTGAAAGGTTTGA
1 TCCTTATTTGAC-ACTTTGAAAGGTTTGA
** * * ** *
24314500 TCCTTACGTGAGCAGATCTGTCCAGGTTTGG
1 TCCTTATTTGA-CA-CTTTG-AAAGGTTTGA
*
24314531 TCCTTCTTTGACCACTTTGAAAGGTTTGA
1 TCCTTATTTGA-CACTTTGAAAGGTTTGA
24314560 TCCT
1 TCCT
24314564 CATGTAAGGG
Statistics
Matches: 45, Mismatches: 16, Indels: 6
0.67 0.24 0.09
Matches are distributed among these distances:
29 21 0.47
30 7 0.16
31 17 0.38
ACGTcount: A:0.19, C:0.20, G:0.20, T:0.40
Consensus pattern (28 bp):
TCCTTATTTGACACTTTGAAAGGTTTGA
Found at i:24314692 original size:40 final size:40
Alignment explanation
Indices: 24314637--24314795 Score: 282
Period size: 40 Copynumber: 4.0 Consensus size: 40
24314627 TTTAAGTAGG
* *
24314637 AAGTTAACATATTTTTAAATCACAAACAAATCTACATCAC
1 AAGTTAACATATTTTTAGATCACAAACAAATTTACATCAC
24314677 AAGTTAACATATTTTTAGATCACAAACAAATTTACATCAC
1 AAGTTAACATATTTTTAGATCACAAACAAATTTACATCAC
24314717 AAGTTAACATATTTTTAGATCACAAACAAATTTACATCAC
1 AAGTTAACATATTTTTAGATCACAAACAAATTTACATCAC
* *
24314757 AAGTTAACATACTTTTAGATCACAAACAAGTTTACATCA
1 AAGTTAACATATTTTTAGATCACAAACAAATTTACATCA
24314796 AACTAGGCAT
Statistics
Matches: 115, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 115 1.00
ACGTcount: A:0.45, C:0.18, G:0.05, T:0.31
Consensus pattern (40 bp):
AAGTTAACATATTTTTAGATCACAAACAAATTTACATCAC
Found at i:24314698 original size:23 final size:22
Alignment explanation
Indices: 24314672--24314781 Score: 87
Period size: 23 Copynumber: 5.3 Consensus size: 22
24314662 ACAAATCTAC
24314672 ATCACAAGTTAACATATTTTTAG
1 ATCACAAGTTAACATA-TTTTAG
* *
24314695 ATCAC-A---AACA-AATTTAC
1 ATCACAAGTTAACATATTTTAG
24314712 ATCACAAGTTAACATATTTTTAG
1 ATCACAAGTTAACATA-TTTTAG
* *
24314735 ATCAC-A---AACA-AATTTAC
1 ATCACAAGTTAACATATTTTAG
24314752 ATCACAAGTTAACATACTTTTAG
1 ATCACAAGTTAACATA-TTTTAG
24314775 ATCACAA
1 ATCACAA
24314782 ACAAGTTTAC
Statistics
Matches: 67, Mismatches: 8, Indels: 24
0.68 0.08 0.24
Matches are distributed among these distances:
17 18 0.27
18 4 0.06
19 8 0.12
21 8 0.12
22 4 0.06
23 25 0.37
ACGTcount: A:0.45, C:0.18, G:0.05, T:0.32
Consensus pattern (22 bp):
ATCACAAGTTAACATATTTTAG
Found at i:24314709 original size:19 final size:19
Alignment explanation
Indices: 24314682--24314749 Score: 59
Period size: 19 Copynumber: 3.5 Consensus size: 19
24314672 ATCACAAGTT
*
24314682 AACATATTTTTAGATCACA
1 AACAAATTTTTAGATCACA
*
24314701 AACAAA--TTTACATCACAA
1 AACAAATTTTTAGATCAC-A
*
24314719 GTTAACATATTTTTAGATCACA
1 ---AACAAATTTTTAGATCACA
24314741 AACAAATTT
1 AACAAATTT
24314750 ACATCACAAG
Statistics
Matches: 38, Mismatches: 5, Indels: 12
0.69 0.09 0.22
Matches are distributed among these distances:
17 9 0.24
18 1 0.03
19 13 0.34
21 5 0.13
22 1 0.03
23 9 0.24
ACGTcount: A:0.46, C:0.16, G:0.04, T:0.34
Consensus pattern (19 bp):
AACAAATTTTTAGATCACA
Found at i:24314715 original size:17 final size:17
Alignment explanation
Indices: 24314690--24314758 Score: 57
Period size: 17 Copynumber: 3.7 Consensus size: 17
24314680 TTAACATATT
*
24314690 TTTAGATCACAAACAAA
1 TTTACATCACAAACAAA
*
24314707 TTTACATCACAAGTTAACATATT
1 TTTACATCAC-A---AACA-A-A
*
24314730 TTTAGATCACAAACAAA
1 TTTACATCACAAACAAA
24314747 TTTACATCACAA
1 TTTACATCACAA
24314759 GTTAACATAC
Statistics
Matches: 41, Mismatches: 5, Indels: 12
0.71 0.09 0.21
Matches are distributed among these distances:
17 20 0.49
18 2 0.05
19 4 0.10
21 4 0.10
22 2 0.05
23 9 0.22
ACGTcount: A:0.46, C:0.19, G:0.04, T:0.30
Consensus pattern (17 bp):
TTTACATCACAAACAAA
Found at i:24315077 original size:18 final size:18
Alignment explanation
Indices: 24315054--24315088 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
24315044 AAAGTACAAG
24315054 AAGTTAACTACAATGCAC
1 AAGTTAACTACAATGCAC
* *
24315072 AAGTTAATTATAATGCA
1 AAGTTAACTACAATGCA
24315089 AGAAGTGAGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.29
Consensus pattern (18 bp):
AAGTTAACTACAATGCAC
Found at i:24320461 original size:55 final size:55
Alignment explanation
Indices: 24320400--24320508 Score: 200
Period size: 55 Copynumber: 2.0 Consensus size: 55
24320390 TGTGGCATAA
24320400 TCTCATGGTGTTATGTCATCAAATTTTGATAAAGCCAAATTTATTGGCCAAAATC
1 TCTCATGGTGTTATGTCATCAAATTTTGATAAAGCCAAATTTATTGGCCAAAATC
* *
24320455 TCTCATGGTGTTATGTCATCGAATTTTGATAAATCCAAATTTATTGGCCAAAAT
1 TCTCATGGTGTTATGTCATCAAATTTTGATAAAGCCAAATTTATTGGCCAAAAT
24320509 AAACTCTCTT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 52 1.00
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.38
Consensus pattern (55 bp):
TCTCATGGTGTTATGTCATCAAATTTTGATAAAGCCAAATTTATTGGCCAAAATC
Found at i:24322066 original size:46 final size:44
Alignment explanation
Indices: 24321962--24322069 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
24321952 TGTCTTTGAC
** * * *
24321962 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
24322006 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
24322052 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
24322070 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:24325835 original size:21 final size:22
Alignment explanation
Indices: 24325811--24325852 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
24325801 AACAATGTCG
24325811 TTTTGTGCA-AAA-TAATTTAAA
1 TTTTGTG-AGAAATTAATTTAAA
*
24325832 TTTTTTGAGAAATTAATTTAA
1 TTTTGTGAGAAATTAATTTAA
24325853 TTACATGTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
20 1 0.06
21 9 0.50
22 8 0.44
ACGTcount: A:0.40, C:0.02, G:0.10, T:0.48
Consensus pattern (22 bp):
TTTTGTGAGAAATTAATTTAAA
Found at i:24329934 original size:15 final size:15
Alignment explanation
Indices: 24329911--24329945 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
24329901 AGATGGAGAT
*
24329911 TATACTATATATATA
1 TATATTATATATATA
24329926 TATATTATATATATA
1 TATATTATATATATA
24329941 -ATATT
1 TATATT
24329946 CATAGCTGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (15 bp):
TATATTATATATATA
Found at i:24334903 original size:30 final size:30
Alignment explanation
Indices: 24334869--24334951 Score: 139
Period size: 30 Copynumber: 2.7 Consensus size: 30
24334859 AAAATTACAT
*
24334869 TTTAATTCTTTAAAAATATAAAAAGTTTGA
1 TTTAATTCTTTAAAAATATAAAAAGTTCGA
*
24334899 TTTAATTCTTTAAAAATATAAAATGTTCGA
1 TTTAATTCTTTAAAAATATAAAAAGTTCGA
24334929 TTTAATTCTTTAAAAATTATAAA
1 TTTAATTCTTTAAAAA-TATAAA
24334952 GATATAGGCT
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
30 44 0.88
31 6 0.12
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.45
Consensus pattern (30 bp):
TTTAATTCTTTAAAAATATAAAAAGTTCGA
Found at i:24346167 original size:136 final size:136
Alignment explanation
Indices: 24345923--24346194 Score: 517
Period size: 136 Copynumber: 2.0 Consensus size: 136
24345913 TGATGGACAG
24345923 CATTGGAATATACATAAGTAAATAATAAAATTATAAATAATATTACCTATAAGCGGGTTGAAGAT
1 CATTGGAATATACATAAGTAAATAATAAAATTATAAATAATATTACCTATAAGCGGGTTGAAGAT
24345988 GAAGTCAATATTGATAAGTGAATGATTTTACAATGATAGATCGAGAACCCGAAGCAATTCGAGGA
66 GAAGTCAATATTGATAAGTGAATGATTTTACAATGATAGATCGAGAACCCGAAGCAATTCGAGGA
24346053 AAATAA
131 AAATAA
* * *
24346059 CATTGGAATATACATAAGTAAATAATGAAATTATAGATAATATTACTTATAAGCGGGTTGAAGAT
1 CATTGGAATATACATAAGTAAATAATAAAATTATAAATAATATTACCTATAAGCGGGTTGAAGAT
24346124 GAAGTCAATATTGATAAGTGAATGATTTTACAATGATAGATCGAGAACCCGAAGCAATTCGAGGA
66 GAAGTCAATATTGATAAGTGAATGATTTTACAATGATAGATCGAGAACCCGAAGCAATTCGAGGA
24346189 AAATAA
131 AAATAA
24346195 AAAATAGCTG
Statistics
Matches: 133, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
136 133 1.00
ACGTcount: A:0.45, C:0.09, G:0.18, T:0.28
Consensus pattern (136 bp):
CATTGGAATATACATAAGTAAATAATAAAATTATAAATAATATTACCTATAAGCGGGTTGAAGAT
GAAGTCAATATTGATAAGTGAATGATTTTACAATGATAGATCGAGAACCCGAAGCAATTCGAGGA
AAATAA
Found at i:24346521 original size:51 final size:51
Alignment explanation
Indices: 24346456--24346569 Score: 210
Period size: 51 Copynumber: 2.2 Consensus size: 51
24346446 AGCGATAAGC
* *
24346456 GACAAGCGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGT
1 GACAAGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGT
24346507 GACAAGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGT
1 GACAAGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGT
24346558 GACAAGTGATAA
1 GACAAGTGATAA
24346570 ATGTGATCAG
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
51 61 1.00
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.28
Consensus pattern (51 bp):
GACAAGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGT
Found at i:24346528 original size:58 final size:56
Alignment explanation
Indices: 24346417--24346563 Score: 196
Period size: 51 Copynumber: 2.7 Consensus size: 56
24346407 TCTGATCAGT
* * *
24346417 GTGGTAGCCTTAGCTACACTTATCTGATCAGCGATAAGCGACAAGCGACAAGTGATAA
1 GTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAG-GA-AAGCGACAAGTGATAA
* *
24346475 GTGGTAGCTTTAGCTACACTTATCTGATCAGTGAC-----AAGTGATAAGTGATAA
1 GTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGGAAAGCGACAAGTGATAA
24346526 GTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAG
1 GTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAG
24346564 TGATAAATGT
Statistics
Matches: 81, Mismatches: 5, Indels: 10
0.84 0.05 0.10
Matches are distributed among these distances:
51 49 0.60
58 32 0.40
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.28
Consensus pattern (56 bp):
GTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGGAAAGCGACAAGTGATAA
Found at i:24349902 original size:438 final size:438
Alignment explanation
Indices: 24349087--24349962 Score: 1734
Period size: 438 Copynumber: 2.0 Consensus size: 438
24349077 TATGTCGTAA
*
24349087 TTGTCCACTAAAAGTGAAAGGCTGTGAATTCCCTGTTGATTTGATGTTGTTACCCTTTCGGGAAT
1 TTGTCCACTAAAAGTGAAAGGCTGTGAATTCCCTGCTGATTTGATGTTGTTACCCTTTCGGGAAT
*
24349152 TTGATATTATTCTGGGGATGGATTGGTTAACAAAACATGACGCTGTAGTGAACTGTCGAGAGAAA
66 TTGATATTATTCTGGGGATGGATTGGTTAACAAAACATGACGCTGTAGTAAACTGTCGAGAGAAA
24349217 CGGATTGATTTGAAAAATCAGACAGGAGAAATAATTTCGGCTGAGTTTGGAAATATGAAAGATAA
131 CGGATTGATTTGAAAAATCAGACAGGAGAAATAATTTCGGCTGAGTTTGGAAATATGAAAGATAA
24349282 TGTCTGAATTATTTCAGCCTTTTCAGCTCAGAAGCTAATGCGGAAGGGTAATGAAGCATATTTAG
196 TGTCTGAATTATTTCAGCCTTTTCAGCTCAGAAGCTAATGCGGAAGGGTAATGAAGCATATTTAG
24349347 CTTATATTTTTTATACTCGGGATTCTAAATCAAAGTTGAAACAGTTGCCAGTTGTTAATGAATTT
261 CTTATATTTTTTATACTCGGGATTCTAAATCAAAGTTGAAACAGTTGCCAGTTGTTAATGAATTT
24349412 GCTGATGTGTTTCCTGAGGAATTGCCGGGTTTACCACCAGATTGTGAAGTTGAGTTTGTGATTGA
326 GCTGATGTGTTTCCTGAGGAATTGCCGGGTTTACCACCAGATTGTGAAGTTGAGTTTGTGATTGA
24349477 TGTGATCCCGGGAACAGCTCCAATATCCGTAACACCATACGGAATGAC
391 TGTGATCCCGGGAACAGCTCCAATATCCGTAACACCATACGGAATGAC
24349525 TTGTCCACTAAAAGTGAAAGGCTGTGAATTCCCTGCTGATTTGATGTTGTTACCCTTTCGGGAAT
1 TTGTCCACTAAAAGTGAAAGGCTGTGAATTCCCTGCTGATTTGATGTTGTTACCCTTTCGGGAAT
24349590 TTGATATTATTCTGGGGATGGATTGGTTAACAAAACATGACGCTGTAGTAAACTGTCGAGAGAAA
66 TTGATATTATTCTGGGGATGGATTGGTTAACAAAACATGACGCTGTAGTAAACTGTCGAGAGAAA
24349655 CGGATTGATTTGAAAAATCAGACAGGAGAAATAATTTCGGCTGAGTTTGGAAATATGAAAGATAA
131 CGGATTGATTTGAAAAATCAGACAGGAGAAATAATTTCGGCTGAGTTTGGAAATATGAAAGATAA
24349720 TGTCTGAATTATTTCAGCCTTTTCAGCTCAGAAGCTAATGCGGAAGGGTAATGAAGCATATTTAG
196 TGTCTGAATTATTTCAGCCTTTTCAGCTCAGAAGCTAATGCGGAAGGGTAATGAAGCATATTTAG
24349785 CTTATATTTTTTATACTCGGGATTCTAAATCAAAGTTGAAACAGTTGCCAGTTGTTAATGAATTT
261 CTTATATTTTTTATACTCGGGATTCTAAATCAAAGTTGAAACAGTTGCCAGTTGTTAATGAATTT
24349850 GCTGATGTGTTTCCTGAGGAATTGCCGGGTTTACCACCAGATTGTGAAGTTGAGTTTGTGATTGA
326 GCTGATGTGTTTCCTGAGGAATTGCCGGGTTTACCACCAGATTGTGAAGTTGAGTTTGTGATTGA
24349915 TGTGATCCCGGGAACAGCTCCAATATCCGTAACACCATACGGAATGAC
391 TGTGATCCCGGGAACAGCTCCAATATCCGTAACACCATACGGAATGAC
24349963 ACCGACTGAA
Statistics
Matches: 436, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
438 436 1.00
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.32
Consensus pattern (438 bp):
TTGTCCACTAAAAGTGAAAGGCTGTGAATTCCCTGCTGATTTGATGTTGTTACCCTTTCGGGAAT
TTGATATTATTCTGGGGATGGATTGGTTAACAAAACATGACGCTGTAGTAAACTGTCGAGAGAAA
CGGATTGATTTGAAAAATCAGACAGGAGAAATAATTTCGGCTGAGTTTGGAAATATGAAAGATAA
TGTCTGAATTATTTCAGCCTTTTCAGCTCAGAAGCTAATGCGGAAGGGTAATGAAGCATATTTAG
CTTATATTTTTTATACTCGGGATTCTAAATCAAAGTTGAAACAGTTGCCAGTTGTTAATGAATTT
GCTGATGTGTTTCCTGAGGAATTGCCGGGTTTACCACCAGATTGTGAAGTTGAGTTTGTGATTGA
TGTGATCCCGGGAACAGCTCCAATATCCGTAACACCATACGGAATGAC
Found at i:24350646 original size:440 final size:440
Alignment explanation
Indices: 24349825--24350704 Score: 1744
Period size: 440 Copynumber: 2.0 Consensus size: 440
24349815 CAAAGTTGAA
24349825 ACAGTTGCCAGTTGTTAATGAATTTGCTGATGTGTTTCCTGAGGAATTGCCGGGTTTACCACCAG
1 ACAGTTGCCAGTTGTTAATGAATTTGCTGATGTGTTTCCTGAGGAATTGCCGGGTTTACCACCAG
24349890 ATTGTGAAGTTGAGTTTGTGATTGATGTGATCCCGGGAACAGCTCCAATATCCGTAACACCATAC
66 ATTGTGAAGTTGAGTTTGTGATTGATGTGATCCCGGGAACAGCTCCAATATCCGTAACACCATAC
24349955 GGAATGACACCGACTGAATTAAAAGAGTTAAAGACTCAGTTGCAAGAATTGTTAGATAAGGGGTT
131 GGAATGACACCGACTGAATTAAAAGAGTTAAAGACTCAGTTGCAAGAATTGTTAGATAAGGGGTT
24350020 TATTAGATCGAGTACATCTCCTTGGGGTGCACCTGTTTTGTTTCTGAAAAAGAAAGATGGTTCGT
196 TATTAGATCGAGTACATCTCCTTGGGGTGCACCTGTTTTGTTTCTGAAAAAGAAAGATGGTTCGT
24350085 TGAGATTGTGTATAGATTACAGACAATTAAATAAGGTTACAATCAAGAACAAATATCCTTTTCCC
261 TGAGATTGTGTATAGATTACAGACAATTAAATAAGGTTACAATCAAGAACAAATATCCTTTTCCC
24350150 CGCATTGATGATTTGTTCGATCAATTGAAAGGTGCTGCTGTGTTTTCAAAAATAGATCTTCGATC
326 CGCATTGATGATTTGTTCGATCAATTGAAAGGTGCTGCTGTGTTTTCAAAAATAGATCTTCGATC
24350215 TGAATATTATCAGCTGAAAGTTAAAGAATGTGACGTGCCAAAAACTACTT
391 TGAATATTATCAGCTGAAAGTTAAAGAATGTGACGTGCCAAAAACTACTT
24350265 ACAGTTGCCAGTTGTTAATGAATTTGCTGATGTGTTTCCTGAGGAATTGCCGGGTTTACCACCAG
1 ACAGTTGCCAGTTGTTAATGAATTTGCTGATGTGTTTCCTGAGGAATTGCCGGGTTTACCACCAG
24350330 ATTGTGAAGTTGAGTTTGTGATTGATGTGATCCCGGGAACAGCTCCAATATCCGTAACACCATAC
66 ATTGTGAAGTTGAGTTTGTGATTGATGTGATCCCGGGAACAGCTCCAATATCCGTAACACCATAC
24350395 GGAATGACACCGACTGAATTAAAAGAGTTAAAGACTCAGTTGCAAGAATTGTTAGATAAGGGGTT
131 GGAATGACACCGACTGAATTAAAAGAGTTAAAGACTCAGTTGCAAGAATTGTTAGATAAGGGGTT
24350460 TATTAGA-CAGAGTACATCTCCTTGGGGTGCACCTGTTTTGTTTCTGAAAAAGAAAGATGGTTCG
196 TATTAGATC-GAGTACATCTCCTTGGGGTGCACCTGTTTTGTTTCTGAAAAAGAAAGATGGTTCG
24350524 TTGAGATTGTGTATAGATTACAGACAATTAAATAAGGTTACAATCAAGAACAAATATCCTTTTCC
260 TTGAGATTGTGTATAGATTACAGACAATTAAATAAGGTTACAATCAAGAACAAATATCCTTTTCC
24350589 CCGCATTGATGATTTGTTCGATCAATTGAAAGGTGCTGCTGTGTTTTCAAAAATAGATCTTCGAT
325 CCGCATTGATGATTTGTTCGATCAATTGAAAGGTGCTGCTGTGTTTTCAAAAATAGATCTTCGAT
24350654 CTGAATATTATCAGCTGAAAGTTAAAGAATGTGACGTGCCAAAAACTACTT
390 CTGAATATTATCAGCTGAAAGTTAAAGAATGTGACGTGCCAAAAACTACTT
24350705 TTAGAACTCG
Statistics
Matches: 439, Mismatches: 0, Indels: 2
1.00 0.00 0.00
Matches are distributed among these distances:
439 1 0.00
440 438 1.00
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (440 bp):
ACAGTTGCCAGTTGTTAATGAATTTGCTGATGTGTTTCCTGAGGAATTGCCGGGTTTACCACCAG
ATTGTGAAGTTGAGTTTGTGATTGATGTGATCCCGGGAACAGCTCCAATATCCGTAACACCATAC
GGAATGACACCGACTGAATTAAAAGAGTTAAAGACTCAGTTGCAAGAATTGTTAGATAAGGGGTT
TATTAGATCGAGTACATCTCCTTGGGGTGCACCTGTTTTGTTTCTGAAAAAGAAAGATGGTTCGT
TGAGATTGTGTATAGATTACAGACAATTAAATAAGGTTACAATCAAGAACAAATATCCTTTTCCC
CGCATTGATGATTTGTTCGATCAATTGAAAGGTGCTGCTGTGTTTTCAAAAATAGATCTTCGATC
TGAATATTATCAGCTGAAAGTTAAAGAATGTGACGTGCCAAAAACTACTT
Found at i:24354849 original size:51 final size:51
Alignment explanation
Indices: 24354773--24354887 Score: 194
Period size: 51 Copynumber: 2.3 Consensus size: 51
24354763 TGAAATTATN
* * *
24354773 TGACAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAG
1 TGACAAGTGATAAGTAATAAGTGGTAGCTTTAACTACACTTATCTGATCAG
*
24354824 TGACAAGTGATAAGTAATAAGTGGTAGTTTTAACTACACTTATCTGATCAG
1 TGACAAGTGATAAGTAATAAGTGGTAGCTTTAACTACACTTATCTGATCAG
24354875 TGACAAGTGATAA
1 TGACAAGTGATAA
24354888 ATGTGATCAG
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 60 1.00
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.30
Consensus pattern (51 bp):
TGACAAGTGATAAGTAATAAGTGGTAGCTTTAACTACACTTATCTGATCAG
Found at i:24357781 original size:16 final size:16
Alignment explanation
Indices: 24357760--24357792 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
24357750 TGGATTTAGG
24357760 TAAGTAACTTATTCAA
1 TAAGTAACTTATTCAA
24357776 TAAGTAACTTATTCAA
1 TAAGTAACTTATTCAA
24357792 T
1 T
24357793 CTAGCCACCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.12, G:0.06, T:0.39
Consensus pattern (16 bp):
TAAGTAACTTATTCAA
Found at i:24361558 original size:16 final size:18
Alignment explanation
Indices: 24361519--24361552 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
24361509 TAAGTTTATA
24361519 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
24361536 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
24361553 AATTTAGAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:24361679 original size:17 final size:17
Alignment explanation
Indices: 24361636--24361684 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
24361626 TTAAGATGAC
24361636 TATATAAAAAATTTCAA
1 TATATAAAAAATTTCAA
*
24361653 TAAATAAAAAATTATCAA
1 TATATAAAAAATT-TCAA
*
24361671 -ATATTAAAATATTT
1 TATA-TAAAAAATTT
24361685 TTAAAAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 15 0.56
18 12 0.44
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (17 bp):
TATATAAAAAATTTCAA
Found at i:24362032 original size:26 final size:27
Alignment explanation
Indices: 24361986--24362044 Score: 68
Period size: 26 Copynumber: 2.2 Consensus size: 27
24361976 AATATTTATA
*
24361986 TTATATTATTTTAATATTTAATAA-TT
1 TTATATTATTTTAATATTTAAAAATTT
* *
24362012 TTATATT-TTTTTATTTATTAAAAATTT
1 TTATATTATTTTAATAT-TTAAAAATTT
24362039 TTATAT
1 TTATAT
24362045 AGTAATCTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 7 0.25
26 13 0.46
27 8 0.29
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (27 bp):
TTATATTATTTTAATATTTAAAAATTT
Found at i:24372142 original size:31 final size:31
Alignment explanation
Indices: 24372106--24372167 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
24372096 GATGCTTGGA
24372106 TTATTATTTTTAATATTTGTATATAATTGTT
1 TTATTATTTTTAATATTTGTATATAATTGTT
24372137 TTATTATTTTTAATATTTGTATATAATTGTT
1 TTATTATTTTTAATATTTGTATATAATTGTT
24372168 GAATTAAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (31 bp):
TTATTATTTTTAATATTTGTATATAATTGTT
Found at i:24374145 original size:31 final size:31
Alignment explanation
Indices: 24374107--24374167 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
24374097 TAACCCGTGT
*
24374107 GATGTCCATCATGAA-GATATCAAAGCCGTTA
1 GATGTCCATCA-CAAGGATATCAAAGCCGTTA
*
24374138 GATGTCCATCACAAGGATATCAGAGCCGTT
1 GATGTCCATCACAAGGATATCAAAGCCGTT
24374168 GATCTTGCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 2 0.07
31 25 0.93
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (31 bp):
GATGTCCATCACAAGGATATCAAAGCCGTTA
Found at i:24380123 original size:24 final size:24
Alignment explanation
Indices: 24380038--24380123 Score: 72
Period size: 23 Copynumber: 3.7 Consensus size: 24
24380028 TTTTTTATTT
* *
24380038 ATTAAAATT-TTTTATATAATCATC
1 ATTAAAATTATTTTATATATTTA-C
*
24380062 -TTAATATTATTTTA-ATATTTAC
1 ATTAAAATTATTTTATATATTTAC
* *
24380084 ATTAAAATAATATTATATATTTA-
1 ATTAAAATTATTTTATATATTTAC
*
24380107 ATATAAATTTATTTTAT
1 AT-TAAAATTATTTTAT
24380124 TAATATATTA
Statistics
Matches: 49, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
22 1 0.02
23 25 0.51
24 23 0.47
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (24 bp):
ATTAAAATTATTTTATATATTTAC
Found at i:24381751 original size:44 final size:44
Alignment explanation
Indices: 24381688--24381776 Score: 151
Period size: 44 Copynumber: 2.0 Consensus size: 44
24381678 CTTGGGAATG
*
24381688 TAAGAACATTGAAAGGAAATTTTAGTGAGTTGCTCAACAGAGAT
1 TAAGAACATTGAAAGGAAATTTTAATGAGTTGCTCAACAGAGAT
* *
24381732 TAAGAGCATTGAAAGGAAATTTTAATGTGTTGCTCAACAGAGAT
1 TAAGAACATTGAAAGGAAATTTTAATGAGTTGCTCAACAGAGAT
24381776 T
1 T
24381777 CAACCAAGAT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.39, C:0.09, G:0.22, T:0.29
Consensus pattern (44 bp):
TAAGAACATTGAAAGGAAATTTTAATGAGTTGCTCAACAGAGAT
Found at i:24385002 original size:14 final size:14
Alignment explanation
Indices: 24384983--24385022 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
24384973 TTGATTGGCA
24384983 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
24384997 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
24385011 GGAAAATGTTTT
1 GTAAAATGTTTT
24385023 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:24385035 original size:34 final size:35
Alignment explanation
Indices: 24384991--24385057 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
24384981 CAGTAAAATG
* *
24384991 TTTTCCGTAAAATGA-TTTCTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGACTTACTGGAAAATATTTTAC
*
24385025 TTTTCTGTAAAATGACTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGACTTACTGGAAAATATTTT
24385058 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 14 0.48
35 15 0.52
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGACTTACTGGAAAATATTTTAC
Found at i:24385044 original size:20 final size:20
Alignment explanation
Indices: 24385006--24385045 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
24384996 CGTAAAATGA
**
24385006 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGACTTACT
*
24385026 TTTCTGTAAAATGACTTACT
1 TTTCTGGAAAATGACTTACT
24385046 GGAAAATATT
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:0.28, C:0.12, G:0.12, T:0.47
Consensus pattern (20 bp):
TTTCTGGAAAATGACTTACT
Found at i:24388198 original size:14 final size:14
Alignment explanation
Indices: 24388179--24388218 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
24388169 NNNNNNNNNN
24388179 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
24388193 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
24388207 GGAAAATGTTTT
1 GTAAAATGTTTT
24388219 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:24388231 original size:34 final size:35
Alignment explanation
Indices: 24388187--24388253 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
24388177 NNGTAAAATG
* *
24388187 TTTTCCGTAAAATGA-TTTCTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGACTTACTGGAAAATATTTTAC
*
24388221 TTTTCTGTAAAATGACTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGACTTACTGGAAAATATTTT
24388254 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 14 0.48
35 15 0.52
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGACTTACTGGAAAATATTTTAC
Found at i:24388240 original size:20 final size:20
Alignment explanation
Indices: 24388202--24388241 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
24388192 CGTAAAATGA
**
24388202 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGACTTACT
*
24388222 TTTCTGTAAAATGACTTACT
1 TTTCTGGAAAATGACTTACT
24388242 GGAAAATATT
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:0.28, C:0.12, G:0.12, T:0.47
Consensus pattern (20 bp):
TTTCTGGAAAATGACTTACT
Found at i:24391634 original size:18 final size:17
Alignment explanation
Indices: 24391592--24391634 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
24391582 TTTGTAAGTT
*
24391592 TATAATATTTTATATTA
1 TATAATTTTTTATATTA
* *
24391609 TGTTATTTTTATATATTA
1 TATAATTTTT-TATATTA
24391627 TATAATTT
1 TATAATTT
24391635 ATAATACATT
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (17 bp):
TATAATTTTTTATATTA
Found at i:24391756 original size:16 final size:17
Alignment explanation
Indices: 24391731--24391773 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 17
24391721 AAATTCAATA
* *
24391731 AATAAAAATATTAAATT
1 AATAATAATATAAAATT
24391748 AA-AATAATATAAAATT
1 AATAATAATATAAAATT
24391764 AATAATAATA
1 AATAATAATA
24391774 ATAATAAAGC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 14 0.61
17 9 0.39
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AATAATAATATAAAATT
Found at i:24393030 original size:20 final size:20
Alignment explanation
Indices: 24393005--24393062 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 20
24392995 GTAATTTAAT
24393005 TTTTATAATTTTTTTACGAA
1 TTTTATAATTTTTTTACGAA
* ***
24393025 TTTTAT-ATTTCTTTACTTT
1 TTTTATAATTTTTTTACGAA
*
24393044 TTTTATAATTTTCTTACGA
1 TTTTATAATTTTTTTACGA
24393063 CTCTATAAAA
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.24, C:0.09, G:0.03, T:0.64
Consensus pattern (20 bp):
TTTTATAATTTTTTTACGAA
Found at i:24395582 original size:29 final size:29
Alignment explanation
Indices: 24395550--24395605 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
24395540 AAGTGGGCTT
*
24395550 TTTTTATT-ATTATAAAAATAACCTTAAAA
1 TTTTGATTAATTATAAAAATAA-CTTAAAA
*
24395579 TTTTGATTAATTATGAAAATAACTTAA
1 TTTTGATTAATTATAAAAATAACTTAA
24395606 TTTTCTAGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 12 0.50
30 12 0.50
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (29 bp):
TTTTGATTAATTATAAAAATAACTTAAAA
Found at i:24396252 original size:34 final size:34
Alignment explanation
Indices: 24396208--24396275 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
24396198 GATAGGCAGC
*
24396208 ACACCAAGTATATTTTTCCTCTCCACCTAGTGTA
1 ACACCAAGTATATTTTTCCTCTCCACCCAGTGTA
*
24396242 ACACCGAGTATATTTTTCCTCTCCACCCAGTGTA
1 ACACCAAGTATATTTTTCCTCTCCACCCAGTGTA
24396276 TTTTTTATGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.25, C:0.31, G:0.10, T:0.34
Consensus pattern (34 bp):
ACACCAAGTATATTTTTCCTCTCCACCCAGTGTA
Found at i:24396443 original size:17 final size:18
Alignment explanation
Indices: 24396406--24396444 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
24396396 TATGTTTTAA
**
24396406 TTTTTTAAGATTTTATGT
1 TTTTTTAAGAAATTATGT
24396424 TTTTTTAAGAAATTAT-T
1 TTTTTTAAGAAATTATGT
24396441 TTTT
1 TTTT
24396445 GTTTTTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.26, C:0.00, G:0.08, T:0.67
Consensus pattern (18 bp):
TTTTTTAAGAAATTATGT
Found at i:24397521 original size:108 final size:108
Alignment explanation
Indices: 24397407--24397715 Score: 564
Period size: 108 Copynumber: 2.9 Consensus size: 108
24397397 GTTTTTTTAA
**
24397407 AATGATATGTTAAGTTAGAATAAGTTTTAAATAATAAAATTTCTAACAAAATTGTATTAAAATTT
1 AATGATATGTTAAGTGGGAATAAGTTTTAAATAATAAAATTTCTAACAAAATTGTATTAAAATTT
*
24397472 TTGTTAATTACTTTGATAAAATTTTTGATTAGTTTAACAAAAC
66 TTGTTAATTACTTTGATAAAATTTTTGATTAGGTTAACAAAAC
24397515 AATGATATGTTAAGTGGGAATAAGTTTTAAATAATAAAATTTCTAACAAAATTGTATTAAAATTT
1 AATGATATGTTAAGTGGGAATAAGTTTTAAATAATAAAATTTCTAACAAAATTGTATTAAAATTT
*
24397580 TTGTTAATTACTTTGATAAAATTTTTGATTAGGTTAACAGAAC
66 TTGTTAATTACTTTGATAAAATTTTTGATTAGGTTAACAAAAC
*
24397623 AATGAGATGTTAAGTGGGAATAAGTTTTAAATAATAAAATTTCTAACAAAATTGTATTAAAATTT
1 AATGATATGTTAAGTGGGAATAAGTTTTAAATAATAAAATTTCTAACAAAATTGTATTAAAATTT
*
24397688 TTGTTAATTACTCTGATAAAATTTTTGA
66 TTGTTAATTACTTTGATAAAATTTTTGA
24397716 AAATTTTTGA
Statistics
Matches: 195, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
108 195 1.00
ACGTcount: A:0.42, C:0.05, G:0.12, T:0.41
Consensus pattern (108 bp):
AATGATATGTTAAGTGGGAATAAGTTTTAAATAATAAAATTTCTAACAAAATTGTATTAAAATTT
TTGTTAATTACTTTGATAAAATTTTTGATTAGGTTAACAAAAC
Found at i:24408932 original size:48 final size:48
Alignment explanation
Indices: 24408853--24408944 Score: 166
Period size: 48 Copynumber: 1.9 Consensus size: 48
24408843 CTAAAGTAAG
*
24408853 CGAGGAGTATATACTTGATTCAGGCTACACCTTCCACATGAGTTAAAT
1 CGAGGAGTATATACTTGATTCAAGCTACACCTTCCACATGAGTTAAAT
*
24408901 CGAGGAGTATATACTTGATTCAAGCTGCACCTTCCACATGAGTT
1 CGAGGAGTATATACTTGATTCAAGCTACACCTTCCACATGAGTT
24408945 CCAATTGGGA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (48 bp):
CGAGGAGTATATACTTGATTCAAGCTACACCTTCCACATGAGTTAAAT
Found at i:24412334 original size:47 final size:47
Alignment explanation
Indices: 24412271--24412362 Score: 175
Period size: 47 Copynumber: 2.0 Consensus size: 47
24412261 TAAATAGACA
24412271 TAGCCTATTCCTCTTGTAACAATTTTATTTTTGAATTCAACATAGAT
1 TAGCCTATTCCTCTTGTAACAATTTTATTTTTGAATTCAACATAGAT
*
24412318 TAGCCTATTCCTCTTGTAACAATTTTATTTTTGAATTCGACATAG
1 TAGCCTATTCCTCTTGTAACAATTTTATTTTTGAATTCAACATAG
24412363 TGAATTTTCT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.28, C:0.17, G:0.10, T:0.45
Consensus pattern (47 bp):
TAGCCTATTCCTCTTGTAACAATTTTATTTTTGAATTCAACATAGAT
Found at i:24425072 original size:32 final size:33
Alignment explanation
Indices: 24425033--24425102 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
24425023 GATAATAAAT
24425033 CTAAATTATTCAATT-AAAAAATAAAACAAACA
1 CTAAATTATTCAATTAAAAAAATAAAACAAACA
* *
24425065 CTAAATTATTCAATTAAAAAAATAAAATAAATA
1 CTAAATTATTCAATTAAAAAAATAAAACAAACA
24425098 CTAAA
1 CTAAA
24425103 AGGGAGGAGG
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
32 15 0.43
33 20 0.57
ACGTcount: A:0.63, C:0.10, G:0.00, T:0.27
Consensus pattern (33 bp):
CTAAATTATTCAATTAAAAAAATAAAACAAACA
Found at i:24432434 original size:17 final size:17
Alignment explanation
Indices: 24432412--24432462 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
24432402 TTTTATTTTT
24432412 ATATAAAAAATTAAAAA
1 ATATAAAAAATTAAAAA
* * *
24432429 ATATAACACA-TCAAAA
1 ATATAAAAAATTAAAAA
24432445 ATACTAAAAACATTAAAA
1 ATA-TAAAAA-ATTAAAA
24432463 TAAATGTTTC
Statistics
Matches: 25, Mismatches: 6, Indels: 4
0.71 0.17 0.11
Matches are distributed among these distances:
16 8 0.32
17 12 0.48
18 1 0.04
19 4 0.16
ACGTcount: A:0.69, C:0.10, G:0.00, T:0.22
Consensus pattern (17 bp):
ATATAAAAAATTAAAAA
Found at i:24435066 original size:17 final size:17
Alignment explanation
Indices: 24435044--24435076 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
24435034 CCTGCAAAAA
*
24435044 CAGAAAGAATAAAAGAG
1 CAGAAACAATAAAAGAG
24435061 CAGAAACAATAAAAGA
1 CAGAAACAATAAAAGA
24435077 AAAATATGTA
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:0.67, C:0.09, G:0.18, T:0.06
Consensus pattern (17 bp):
CAGAAACAATAAAAGAG
Found at i:24436616 original size:46 final size:46
Alignment explanation
Indices: 24436566--24436728 Score: 263
Period size: 46 Copynumber: 3.5 Consensus size: 46
24436556 CATTTTCTGT
** * **
24436566 CATGGTCTTATTCTTTTCATATCACATTGCCATGGTATCTTTCAAC
1 CATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAAC
**
24436612 CATGGTCTTATTCATTTCATATCAGGTTGCCATGGTATCTTTCAAC
1 CATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAAC
24436658 CATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAAC
1 CATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAAC
24436704 CATGGTCTTACACATTTCATATCAG
1 CATGGTCTTACACATTTCATATCAG
24436729 AGAGCACACT
Statistics
Matches: 112, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 112 1.00
ACGTcount: A:0.23, C:0.23, G:0.13, T:0.40
Consensus pattern (46 bp):
CATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAAC
Found at i:24436844 original size:54 final size:54
Alignment explanation
Indices: 24436762--24436898 Score: 247
Period size: 54 Copynumber: 2.5 Consensus size: 54
24436752 TCCTTACAGT
* * *
24436762 GGGATTACCAGTCTAGGCTAAATCCCCTGTAGTATAAACTCGTAGAGTATTGTC
1 GGGATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACTCATAGAGTATTGTC
24436816 GGGATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACTCATAGAGTATTGTC
1 GGGATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACTCATAGAGTATTGTC
24436870 GGGATTACCAGTCCAGGCTAAATCCCCTG
1 GGGATTACCAGTCCAGGCTAAATCCCCTG
24436899 CAACGACAAT
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 80 1.00
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.27
Consensus pattern (54 bp):
GGGATTACCAGTCCAGGCTAAATCCCCTGTAATATAAACTCATAGAGTATTGTC
Found at i:24443619 original size:10 final size:10
Alignment explanation
Indices: 24443597--24443629 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
24443587 TACTTCATAG
24443597 AAAATTA-AA
1 AAAATTAGAA
24443606 AAAATTAGAA
1 AAAATTAGAA
24443616 AAAATTAGAA
1 AAAATTAGAA
24443626 AAAA
1 AAAA
24443630 AACATAAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 7 0.30
10 16 0.70
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (10 bp):
AAAATTAGAA
Found at i:24444964 original size:15 final size:15
Alignment explanation
Indices: 24444914--24444969 Score: 53
Period size: 15 Copynumber: 3.6 Consensus size: 15
24444904 TTTTTTATTG
24444914 TTTAT-TTTAAATTGT
1 TTTATATTTAAATT-T
*
24444929 ATTTATATTGATAAATAT
1 -TTTATATT--TAAATTT
24444947 TTTATATTTAAATTT
1 TTTATATTTAAATTT
24444962 TTTA-ATTT
1 TTTATATTT
24444970 TATATATAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
14 4 0.11
15 10 0.29
16 5 0.14
17 10 0.29
18 1 0.03
19 5 0.14
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (15 bp):
TTTATATTTAAATTT
Found at i:24444982 original size:20 final size:21
Alignment explanation
Indices: 24444945--24444986 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
24444935 ATTGATAAAT
*
24444945 ATTTTATATTTAAATTTTTTA
1 ATTTTATATATAAATTTTTTA
24444966 ATTTTATATAT-AATTTTTTA
1 ATTTTATATATAAATTTTTTA
24444986 A
1 A
24444987 ATATCAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
ATTTTATATATAAATTTTTTA
Found at i:24445378 original size:21 final size:21
Alignment explanation
Indices: 24445348--24445387 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
24445338 ATTCTAAAAT
*
24445348 TATTTTTAT-ATTAATATTTTA
1 TATTTGTATAATTAA-ATTTTA
24445369 TATTTGTATAATTAAATTT
1 TATTTGTATAATTAAATTT
24445388 AAACATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (21 bp):
TATTTGTATAATTAAATTTTA
Found at i:24456393 original size:15 final size:15
Alignment explanation
Indices: 24456373--24456404 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
24456363 TATTATATCG
*
24456373 CTCACTGCTTATTAT
1 CTCACTGCTCATTAT
24456388 CTCACTGCTCATTAT
1 CTCACTGCTCATTAT
24456403 CT
1 CT
24456405 TCTCAGGACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.31, G:0.06, T:0.44
Consensus pattern (15 bp):
CTCACTGCTCATTAT
Found at i:24464586 original size:3 final size:3
Alignment explanation
Indices: 24464580--24464605 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
24464570 TTTTTTTTAA
24464580 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
24464606 AAAATTCAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:24465830 original size:22 final size:22
Alignment explanation
Indices: 24465783--24465830 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
24465773 ATTTTGTTTC
* **
24465783 TAAAATTTTGAAATAATTTATT
1 TAAAATTTTGAAATAAATTAAA
24465805 TAAAATTTTGAAATAAATTAAA
1 TAAAATTTTGAAATAAATTAAA
24465827 TAAA
1 TAAA
24465831 TTTAATTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (22 bp):
TAAAATTTTGAAATAAATTAAA
Found at i:24466836 original size:33 final size:33
Alignment explanation
Indices: 24466784--24467015 Score: 177
Period size: 33 Copynumber: 7.0 Consensus size: 33
24466774 TATCTTCAGC
* *
24466784 CCACCATC-GTACTCCGCTCCTTCCGGCTCGTAT
1 CCACCA-CAGTACTCCACTCCTTCCAGCTCGTAT
* **
24466817 CCACCACAGTATTCTGCTCCTTCCAGCTCGTAT
1 CCACCACAGTACTCCACTCCTTCCAGCTCGTAT
* * * *
24466850 CAACCACCA-TACTCCGCTCCTTCTATCTCGTAT
1 CCACCA-CAGTACTCCACTCCTTCCAGCTCGTAT
* * *
24466883 CCACCACCGTACTCCACTCCTTCTAACTCGTAT
1 CCACCACAGTACTCCACTCCTTCCAGCTCGTAT
* **
24466916 CCACCACCGTACTCCACTCCTTCTGGCTCGTAT
1 CCACCACAGTACTCCACTCCTTCCAGCTCGTAT
* * * * * *
24466949 CCATCGACA-TTCTCTACTCCTCCCGGCTTGTAT
1 CCA-CCACAGTACTCCACTCCTTCCAGCTCGTAT
* *
24466982 CCACCACCA-TACTCTACTCC-TCCAGAGTCGTAT
1 CCACCA-CAGTACTCCACTCCTTCCAG-CTCGTAT
24467015 C
1 C
24467016 TACCTTCGTT
Statistics
Matches: 166, Mismatches: 27, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
32 7 0.04
33 154 0.93
34 5 0.03
ACGTcount: A:0.18, C:0.43, G:0.10, T:0.28
Consensus pattern (33 bp):
CCACCACAGTACTCCACTCCTTCCAGCTCGTAT
Found at i:24466903 original size:66 final size:66
Alignment explanation
Indices: 24466784--24466995 Score: 228
Period size: 66 Copynumber: 3.2 Consensus size: 66
24466774 TATCTTCAGC
* * * * * *
24466784 CCACCATCGTACTCCGCTCCTTCCGGCTCGTATCCACCACAGTATTCTGCTCCTTCCAGCTCGTA
1 CCACCACCATACTCCGCTCCTTCTGGCTCGTATCCACCACCGTACTCTACTCCTTCCAGCTCGTA
24466849 T
66 T
* ** * * *
24466850 CAACCACCATACTCCGCTCCTTCTATCTCGTATCCACCACCGTACTCCACTCCTTCTAACTCGTA
1 CCACCACCATACTCCGCTCCTTCTGGCTCGTATCCACCACCGTACTCTACTCCTTCCAGCTCGTA
24466915 T
66 T
* * * * * * * *
24466916 CCACCACCGTACTCCACTCCTTCTGGCTCGTATCCATCGA-CATTCTCTACTCCTCCCGGCTTGT
1 CCACCACCATACTCCGCTCCTTCTGGCTCGTATCCA-CCACCGTACTCTACTCCTTCCAGCTCGT
24466980 AT
65 AT
24466982 CCACCACCATACTC
1 CCACCACCATACTC
24466996 TACTCCTCCA
Statistics
Matches: 118, Mismatches: 27, Indels: 2
0.80 0.18 0.01
Matches are distributed among these distances:
66 116 0.98
67 2 0.02
ACGTcount: A:0.18, C:0.44, G:0.10, T:0.28
Consensus pattern (66 bp):
CCACCACCATACTCCGCTCCTTCTGGCTCGTATCCACCACCGTACTCTACTCCTTCCAGCTCGTA
T
Found at i:24466935 original size:38 final size:33
Alignment explanation
Indices: 24466784--24466951 Score: 183
Period size: 33 Copynumber: 5.1 Consensus size: 33
24466774 TATCTTCAGC
* * ***
24466784 CCACCATCGTACTCCGCTCCTTCCGGCTCGTAT
1 CCACCACCGTACTCCACTCCTTCTAACTCGTAT
* * ** * *
24466817 CCACCACAGTATTCTGCTCCTTCCAGCTCGTAT
1 CCACCACCGTACTCCACTCCTTCTAACTCGTAT
* * * *
24466850 CAACCACCATACTCCGCTCCTTCTATCTCGTAT
1 CCACCACCGTACTCCACTCCTTCTAACTCGTAT
24466883 CCACCACCGTACTCCACTCCTTCTAACTCGTAT
1 CCACCACCGTACTCCACTCCTTCTAACTCGTAT
**
24466916 CCACCACCGTACTCCACTCCTTCTGGCTCGTAT
1 CCACCACCGTACTCCACTCCTTCTAACTCGTAT
24466949 CCA
1 CCA
24466952 TCGACATTCT
Statistics
Matches: 117, Mismatches: 18, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 117 1.00
ACGTcount: A:0.18, C:0.44, G:0.10, T:0.28
Consensus pattern (33 bp):
CCACCACCGTACTCCACTCCTTCTAACTCGTAT
Found at i:24466969 original size:99 final size:99
Alignment explanation
Indices: 24466784--24467015 Score: 216
Period size: 99 Copynumber: 2.3 Consensus size: 99
24466774 TATCTTCAGC
* * ** * **
24466784 CCACCATCGTACTCCGCTCCTTCCGGCTCGTATCCACCACAGTATTCTGCTCCTTCCAGCTCGTA
1 CCACCACCGTACTCCACTCCTTCCAACTCGTATCCACCACAGTACTCCACTCCTTCCAGCTCGTA
* * * *
24466849 TCAACCACCATACTCCGCTCCTTCTATCTCGTAT
66 TCAACCACCATACTCCACTCCTCCCAGCTCGTAT
* * **
24466883 CCACCACCGTACTCCACTCCTTCTAACTCGTATCCACCACCGTACTCCACTCCTTCTGGCTCGTA
1 CCACCACCGTACTCCACTCCTTCCAACTCGTATCCACCACAGTACTCCACTCCTTCCAGCTCGTA
* * * * * *
24466948 TCCATCGA-CATTCTCTACTCCTCCCGGCTTGTAT
66 T-CAACCACCATACTCCACTCCTCCCAGCTCGTAT
* * *
24466982 CCACCACCATACTCTACTCC-TCCAGAGTCGTATC
1 CCACCACCGTACTCCACTCCTTCCA-ACTCGTATC
24467016 TACCTTCGTT
Statistics
Matches: 106, Mismatches: 25, Indels: 4
0.79 0.19 0.03
Matches are distributed among these distances:
98 3 0.03
99 99 0.93
100 4 0.04
ACGTcount: A:0.18, C:0.43, G:0.10, T:0.28
Consensus pattern (99 bp):
CCACCACCGTACTCCACTCCTTCCAACTCGTATCCACCACAGTACTCCACTCCTTCCAGCTCGTA
TCAACCACCATACTCCACTCCTCCCAGCTCGTAT
Found at i:24470301 original size:21 final size:19
Alignment explanation
Indices: 24470249--24470302 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 19
24470239 AGCACCTTAT
24470249 TTTTCTTCTTCTTCTTTTCC
1 TTTT-TTCTTCTTCTTTTCC
*
24470269 TTTCTTCCCTTCTTCTTTCTCTC
1 TTT-TT-TCTTCTTCTTT-TC-C
24470292 TTTTTTCTTCT
1 TTTTTTCTTCT
24470303 GCTAATTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
20 4 0.14
21 16 0.57
22 4 0.14
23 4 0.14
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTTTTCTTCTTCTTTTCC
Found at i:24472686 original size:42 final size:42
Alignment explanation
Indices: 24472625--24472780 Score: 156
Period size: 42 Copynumber: 3.6 Consensus size: 42
24472615 TCGTTTTCTC
** *
24472625 GATGCCATAGTTCAACTATGGTCTTACACATATTCACATAAT
1 GATGCCATAGCCCAGCTATGGTCTTACACATATTCACATAAT
* *
24472667 GATGCCATAGCCCAGCTATGGTCGTACACATATTCATAT-AT
1 GATGCCATAGCCCAGCTATGGTCTTACACATATTCACATAAT
*
24472708 CGATGCTATAGCCCAGCTATGGTCTTACACGA-A-TCACATATCTCACT
1 -GATGCCATAGCCCAGCTATGGTCTTACAC-ATATTCACATA----A-T
* *
24472755 GATGCCATATCCCAGATATGGTCTTA
1 GATGCCATAGCCCAGCTATGGTCTTA
24472781 TACAGTAGCA
Statistics
Matches: 95, Mismatches: 11, Indels: 12
0.81 0.09 0.10
Matches are distributed among these distances:
41 7 0.07
42 62 0.65
43 1 0.01
46 24 0.25
47 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.30
Consensus pattern (42 bp):
GATGCCATAGCCCAGCTATGGTCTTACACATATTCACATAAT
Found at i:24472793 original size:88 final size:90
Alignment explanation
Indices: 24472666--24472877 Score: 209
Period size: 88 Copynumber: 2.3 Consensus size: 90
24472656 ATTCACATAA
* * * * * * *
24472666 TGATGCCATAGCCCAGCTATGGTCGTACACATATTCATATAT-CGATGCTATAGCCCAGCTATGG
1 TGATGCCATATCCCAGATATGGTCTTATACATATGCATATATCCGATGCCATAGCCCAGATATGG
24472730 TCTTACAC-G-AATCACATATCTCAC-
66 TCTTACACGGAAATCAC-T-TCTCACT
*
24472754 TGATGCCATATCCCAGATATGGTCTTATACAGTA-GCATATATCACACCGATGCCATATCCCAGA
1 TGATGCCATATCCCAGATATGGTCTTATACA-TATGCATATAT----CCGATGCCATAGCCCAGA
* *
24472818 TATGGTCTTATACGGAAATCACTTGTCACT
61 TATGGTCTTACACGGAAATCACTTCTCACT
* * *
24472848 TGTTGTCATATCCTAGATATGGTCTTATAC
1 TGATGCCATATCCCAGATATGGTCTTATAC
24472878 GGAAATAACT
Statistics
Matches: 102, Mismatches: 13, Indels: 12
0.80 0.10 0.09
Matches are distributed among these distances:
88 34 0.33
89 2 0.02
93 31 0.30
94 29 0.28
95 6 0.06
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (90 bp):
TGATGCCATATCCCAGATATGGTCTTATACATATGCATATATCCGATGCCATAGCCCAGATATGG
TCTTACACGGAAATCACTTCTCACT
Found at i:24472811 original size:47 final size:46
Alignment explanation
Indices: 24472708--24472831 Score: 158
Period size: 47 Copynumber: 2.7 Consensus size: 46
24472698 ATTCATATAT
* * * * * *
24472708 CGATGCTATAGCCCAGCTATGGTCTTACACGAATCACATATCTCAC
1 CGATGCCATATCCCAGATATGGTCTTATACGAAGCACATATCACAC
* * *
24472754 TGATGCCATATCCCAGATATGGTCTTATACAGTAGCATATATCACAC
1 CGATGCCATATCCCAGATATGGTCTTATAC-GAAGCACATATCACAC
24472801 CGATGCCATATCCCAGATATGGTCTTATACG
1 CGATGCCATATCCCAGATATGGTCTTATACG
24472832 GAAATCACTT
Statistics
Matches: 67, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
46 26 0.39
47 41 0.61
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.28
Consensus pattern (46 bp):
CGATGCCATATCCCAGATATGGTCTTATACGAAGCACATATCACAC
Found at i:24472858 original size:47 final size:47
Alignment explanation
Indices: 24472807--24472897 Score: 164
Period size: 47 Copynumber: 1.9 Consensus size: 47
24472797 ACACCGATGC
*
24472807 CATATCCCAGATATGGTCTTATACGGAAATCACTTGTCACTTGTTGT
1 CATATCCCAGATATGGTCTTATACGGAAATAACTTGTCACTTGTTGT
*
24472854 CATATCCTAGATATGGTCTTATACGGAAATAACTTGTCACTTGT
1 CATATCCCAGATATGGTCTTATACGGAAATAACTTGTCACTTGT
24472898 CACTTGTAGC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 42 1.00
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.36
Consensus pattern (47 bp):
CATATCCCAGATATGGTCTTATACGGAAATAACTTGTCACTTGTTGT
Found at i:24472875 original size:94 final size:93
Alignment explanation
Indices: 24472708--24472877 Score: 227
Period size: 93 Copynumber: 1.8 Consensus size: 93
24472698 ATTCATATAT
* *
24472708 CGATGCTATAGCCCAGCTATGGTCTTACACGAATCACATATCTCACTGATGCCATATCCCAGATA
1 CGATGCCATAGCCCAGATATGGTCTTACACGAATCACATATCTCACTGATGCCATATCCCAGATA
24472773 TGGTCTTATACAGTAGCATATATCACAC
66 TGGTCTTATACAGTAGCATATATCACAC
* * * * * *
24472801 CGATGCCATATCCCAGATATGGTCTTATACGGAAATCAC-T-TGTCACTTGTTGTCATATCCTAG
1 CGATGCCATAGCCCAGATATGGTCTTACAC-G-AATCACATATCTCAC-TGATGCCATATCCCAG
24472864 ATATGGTCTTATAC
63 ATATGGTCTTATAC
24472878 GGAAATAACT
Statistics
Matches: 66, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
93 31 0.47
94 29 0.44
95 6 0.09
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (93 bp):
CGATGCCATAGCCCAGATATGGTCTTACACGAATCACATATCTCACTGATGCCATATCCCAGATA
TGGTCTTATACAGTAGCATATATCACAC
Found at i:24472946 original size:31 final size:31
Alignment explanation
Indices: 24472911--24473082 Score: 215
Period size: 31 Copynumber: 5.5 Consensus size: 31
24472901 TTGTAGCCGA
* *
24472911 AGCTACCACTATTCACTAATCAGGTAGACGG
1 AGCTACCACTTTTCACTGATCAGGTAGACGG
* * *
24472942 AGCTACCATTTTTTCAATGATCAGGTAGCCGG
1 AGCTACCA-CTTTTCACTGATCAGGTAGACGG
*
24472974 AGCTA-CACTTTTCACTGATCAGGTAGCCGG
1 AGCTACCACTTTTCACTGATCAGGTAGACGG
* *
24473004 AACTACCACTTTTCACTGATCAGGTA-ACAGA
1 AGCTACCACTTTTCACTGATCAGGTAGAC-GG
*
24473035 AGCTACCACTTTTCACTGATCAGGTAG-CTGA
1 AGCTACCACTTTTCACTGATCAGGTAGAC-GG
24473066 AGCTACCACTTTTCACT
1 AGCTACCACTTTTCACT
24473083 TGTCATTTGT
Statistics
Matches: 125, Mismatches: 12, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
30 26 0.21
31 76 0.61
32 23 0.18
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (31 bp):
AGCTACCACTTTTCACTGATCAGGTAGACGG
Found at i:24473013 original size:93 final size:93
Alignment explanation
Indices: 24472903--24473082 Score: 249
Period size: 93 Copynumber: 1.9 Consensus size: 93
24472893 CTTGTCACTT
* *
24472903 GTAGCCGAAGCTACCACTATTCACTAATCAGGTAGAC-GGAGCTACCATTTTTTCAATGATCAGG
1 GTAGCCGAAGCTACCACTATTCACTAATCAGGTA-ACAGAAGCTACCA-CTTTTCAATGATCAGG
*
24472967 TAGCCGGAGCTA-CACTTTTCACTGATCAG
64 TAGCCGAAGCTACCACTTTTCACTGATCAG
* * *
24472996 GTAGCCGGAA-CTACCACTTTTCACTGATCAGGTAACAGAAGCTACCACTTTTCACTGATCAGGT
1 GTAGCC-GAAGCTACCACTATTCACTAATCAGGTAACAGAAGCTACCACTTTTCAATGATCAGGT
*
24473060 AGCTGAAGCTACCACTTTTCACT
65 AGCCGAAGCTACCACTTTTCACT
24473083 TGTCATTTGT
Statistics
Matches: 77, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
92 26 0.34
93 48 0.62
94 3 0.04
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.27
Consensus pattern (93 bp):
GTAGCCGAAGCTACCACTATTCACTAATCAGGTAACAGAAGCTACCACTTTTCAATGATCAGGTA
GCCGAAGCTACCACTTTTCACTGATCAG
Found at i:24473164 original size:50 final size:51
Alignment explanation
Indices: 24473058--24473186 Score: 199
Period size: 50 Copynumber: 2.5 Consensus size: 51
24473048 CACTGATCAG
* * *
24473058 GTAGCTGAAGCTACCACTTTTCACTTGTCATTTGTCATTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTCATTTGTCATTGATCAGATAAGT
*
24473109 GTAGCCGAAGCTATCACTTATCACTT-TCACTTT-TCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTCA-TTTGTCATTGATCAGATAAGT
24473159 GTAGCCGAAGCTATCACTTATCACTTGT
1 GTAGCCGAAGCTATCACTTATCACTTGT
24473187 TGCCATGGTC
Statistics
Matches: 72, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
50 45 0.62
51 27 0.38
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (51 bp):
GTAGCCGAAGCTATCACTTATCACTTGTCATTTGTCATTGATCAGATAAGT
Found at i:24476201 original size:14 final size:14
Alignment explanation
Indices: 24476182--24476208 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
24476172 GAGTTCTTTT
24476182 GTTGAAGATGAGTC
1 GTTGAAGATGAGTC
24476196 GTTGAAGATGAGT
1 GTTGAAGATGAGT
24476209 ACATGAATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.04, G:0.37, T:0.30
Consensus pattern (14 bp):
GTTGAAGATGAGTC
Found at i:24478311 original size:30 final size:30
Alignment explanation
Indices: 24478277--24478336 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
24478267 TATTTTATTA
*
24478277 TTAATTTTGTTATTATTTTAAAGATATTTG
1 TTAATTTTGTTATTATTTTAAAGACATTTG
*
24478307 TTAATTTTGTTATTATTTTAGAGACATTTG
1 TTAATTTTGTTATTATTTTAAAGACATTTG
24478337 CTTGTTAAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.28, C:0.02, G:0.12, T:0.58
Consensus pattern (30 bp):
TTAATTTTGTTATTATTTTAAAGACATTTG
Found at i:24478728 original size:26 final size:26
Alignment explanation
Indices: 24478692--24478747 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
24478682 TTAATCAATT
24478692 TATAAATAATATTTCTAAAAAAGTGA
1 TATAAATAATATTTCTAAAAAAGTGA
*
24478718 TATAAATAATATTTCTAGAAAAGTGA
1 TATAAATAATATTTCTAAAAAAGTGA
24478744 TATA
1 TATA
24478748 GAAACAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.52, C:0.04, G:0.09, T:0.36
Consensus pattern (26 bp):
TATAAATAATATTTCTAAAAAAGTGA
Found at i:24479801 original size:22 final size:22
Alignment explanation
Indices: 24479760--24479806 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
24479750 TTACATAGTA
*
24479760 AAATGTGATTAAATCCAAAATT
1 AAATGTGATTAAATCCAAAAAT
*
24479782 AAATG-GATTAAATCGTAAAAAT
1 AAATGTGATTAAATC-CAAAAAT
24479804 AAA
1 AAA
24479807 ATAAAACTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.55, C:0.06, G:0.11, T:0.28
Consensus pattern (22 bp):
AAATGTGATTAAATCCAAAAAT
Found at i:24481916 original size:132 final size:132
Alignment explanation
Indices: 24481665--24482148 Score: 833
Period size: 132 Copynumber: 3.7 Consensus size: 132
24481655 GTGGCTACTT
* * *
24481665 TAGAAAACCCTCAAGTTGTTGAAATTAATCCTGGCATGGGAGTAAATTTTGAAGAATGTTCTCAG
1 TAGAAAACCCACAAGTTGATGAAATTAATCCTGGCATGGGAGAAAATTTTGAAGAATGTTCTCAG
* * * * *
24481730 CTTCATCCCTCTAATCAAGGAGAGGCTAGGTTGGAGGAAGGTACCCTCGTGGCTACTTTATCAAC
66 CTTCATCCCTCTAATCAAGGAGAGGCTAGGTCGGAGGAAGTTTCCCTTGCGGCTACTTTATCAAC
*
24481795 CG
131 TG
* * *
24481797 TAGAAAACCCTCAAGTTGTTGAAATTAATCCTGGCGTGGGAGAAAATTTTGAAGAATGTTCTCAG
1 TAGAAAACCCACAAGTTGATGAAATTAATCCTGGCATGGGAGAAAATTTTGAAGAATGTTCTCAG
24481862 CTTCATCCCTCTAATCAAGGAGAGGCTAGGTCGGAGGAAGTTTCCCTTGCGGCTACTTTATCAAC
66 CTTCATCCCTCTAATCAAGGAGAGGCTAGGTCGGAGGAAGTTTCCCTTGCGGCTACTTTATCAAC
24481927 TG
131 TG
* *
24481929 TAGAAACCCCACAAGTTGATGAAATTAATCCTGGCGTGGGAGAAAATTTTGAAGAATGTTCTCAG
1 TAGAAAACCCACAAGTTGATGAAATTAATCCTGGCATGGGAGAAAATTTTGAAGAATGTTCTCAG
24481994 CTTCATCCCTCTAATCAAGGAGAGGCTAGGTCGGAGGAAGTTTCCCTTGCGGCTACTTTATCAAC
66 CTTCATCCCTCTAATCAAGGAGAGGCTAGGTCGGAGGAAGTTTCCCTTGCGGCTACTTTATCAAC
24482059 TG
131 TG
*
24482061 TAGAAACCCCACAAGTTGATGAAATTAATCCTGGCATGGGAGAAAATTTTGAAGAATGTTCTCAG
1 TAGAAAACCCACAAGTTGATGAAATTAATCCTGGCATGGGAGAAAATTTTGAAGAATGTTCTCAG
24482126 CTTCATCCCTCTAATCAAGGAGA
66 CTTCATCCCTCTAATCAAGGAGA
24482149 TATGCTCGTG
Statistics
Matches: 340, Mismatches: 12, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
132 340 1.00
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.28
Consensus pattern (132 bp):
TAGAAAACCCACAAGTTGATGAAATTAATCCTGGCATGGGAGAAAATTTTGAAGAATGTTCTCAG
CTTCATCCCTCTAATCAAGGAGAGGCTAGGTCGGAGGAAGTTTCCCTTGCGGCTACTTTATCAAC
TG
Found at i:24484802 original size:5 final size:5
Alignment explanation
Indices: 24484792--24484817 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
24484782 TTTTTAAATA
24484792 TTTAT TTTAT TTTAT TTTAT TTTAT T
1 TTTAT TTTAT TTTAT TTTAT TTTAT T
24484818 AGTTAATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:24494326 original size:6 final size:6
Alignment explanation
Indices: 24494306--24494337 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
24494296 ATAAAATACA
24494306 ATAT-G ATAT-G ATATAG ATATAG ATATAG ATAT
1 ATATAG ATATAG ATATAG ATATAG ATATAG ATAT
24494338 TGGAACGCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 9 0.35
6 17 0.65
ACGTcount: A:0.47, C:0.00, G:0.16, T:0.38
Consensus pattern (6 bp):
ATATAG
Found at i:24494531 original size:16 final size:17
Alignment explanation
Indices: 24494506--24494545 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
24494496 AACTCGATTG
*
24494506 AATA-TTTAAATCTAA-
1 AATATTTTAAATATAAT
24494521 AATATTTTAAATATAAT
1 AATATTTTAAATATAAT
24494538 AATATTTT
1 AATATTTT
24494546 GATAAGATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 4 0.18
16 10 0.45
17 8 0.36
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
AATATTTTAAATATAAT
Found at i:24496031 original size:3 final size:3
Alignment explanation
Indices: 24496023--24496055 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
24496013 AATCCCACTT
24496023 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
24496056 TGAAATAAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:24497429 original size:22 final size:23
Alignment explanation
Indices: 24497404--24497450 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
24497394 CTAAATTTGA
24497404 TTTAAA-TAATAAAAAAAATATT
1 TTTAAATTAATAAAAAAAATATT
* *
24497426 TTTAAATTTAATTATAAAAATATT
1 TTTAAA-TTAATAAAAAAAATATT
24497450 T
1 T
24497451 AAATATTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 6 0.29
24 15 0.71
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TTTAAATTAATAAAAAAAATATT
Found at i:24497444 original size:23 final size:23
Alignment explanation
Indices: 24497403--24497467 Score: 73
Period size: 22 Copynumber: 2.9 Consensus size: 23
24497393 TCTAAATTTG
* *
24497403 ATTTAAATAATAA-AAAAAATAT
1 ATTTAAATATTAATATAAAATAT
*
24497425 TTTTAAAT-TTAATTATAAAA-AT
1 ATTTAAATATTAA-TATAAAATAT
24497447 ATTTAAATATTAATATAAAAT
1 ATTTAAATATTAATATAAAAT
24497468 GCTTTTATTA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
21 3 0.09
22 23 0.66
23 9 0.26
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
ATTTAAATATTAATATAAAATAT
Found at i:24500071 original size:30 final size:30
Alignment explanation
Indices: 24500037--24500098 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
24500027 CACCAAGTGA
*
24500037 GTTAATCCTTGCCTTTTTCTTGTAATTTTT
1 GTTAATCATTGCCTTTTTCTTGTAATTTTT
24500067 GTTAATCATTGCCTTTTTCTTGTAATTTTT
1 GTTAATCATTGCCTTTTTCTTGTAATTTTT
24500097 GT
1 GT
24500099 GTTTCTAAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.15, C:0.15, G:0.11, T:0.60
Consensus pattern (30 bp):
GTTAATCATTGCCTTTTTCTTGTAATTTTT
Found at i:24505191 original size:14 final size:14
Alignment explanation
Indices: 24505174--24505200 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
24505164 TCAATCGAGT
24505174 TTTTTTTATTTTAG
1 TTTTTTTATTTTAG
24505188 TTTTTTTATTTTA
1 TTTTTTTATTTTA
24505201 TTCATTTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.04, T:0.81
Consensus pattern (14 bp):
TTTTTTTATTTTAG
Found at i:24505377 original size:30 final size:32
Alignment explanation
Indices: 24505343--24505416 Score: 91
Period size: 34 Copynumber: 2.3 Consensus size: 32
24505333 ATATTTATAT
24505343 TTTCTTTTAAATCTA-TTTA-TATATAATTTA
1 TTTCTTTTAAATCTATTTTACTATATAATTTA
* *
24505373 TTTCTTTTAAAGATCTATTTTACTATATATTTTG
1 TTTCTTTT-AA-ATCTATTTTACTATATAATTTA
24505407 TTT-TTTTAAA
1 TTTCTTTTAAA
24505417 CACTCTCATC
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
30 8 0.21
31 3 0.08
32 7 0.18
33 8 0.21
34 12 0.32
ACGTcount: A:0.30, C:0.07, G:0.03, T:0.61
Consensus pattern (32 bp):
TTTCTTTTAAATCTATTTTACTATATAATTTA
Found at i:24517221 original size:163 final size:163
Alignment explanation
Indices: 24516922--24517246 Score: 472
Period size: 162 Copynumber: 2.0 Consensus size: 163
24516912 TTGTTCATTT
* * * * * * * *
24516922 CAATTGGTATCAGAGTGAGCTTTAAGAGTTACTTGAAGATGATTCTTTGTACAATTTGCAACCGT
1 CAATTAGTATCAAAATGAGCTTCAAGAGTTAATTAAAGACGATTCTTTGTACAATTTGCAACCAT
* * * * * *
24516987 GGAATCCATGAAAAAAGTTTCATCTCTCAAGTTCCAATACTAATTGGATCCTTAAACTATGCTTG
66 GGAATCCATAAAAAAAATTTCATCTCTCAAGCTCCAATACTAATTGCATCCTCAAACTATGCTTA
24517052 TTGGAAAGCTC-AAATCAAGGCTTTCATAATGA
131 TTGGAAAGCTCAAAATCAAGGCTTTCATAATGA
* * *
24517084 CAATTAGTATCAAAATGAGCTTCAAGAGTTAATTAAAGACGATTCTTTGTATAATTTGTAACTAT
1 CAATTAGTATCAAAATGAGCTTCAAGAGTTAATTAAAGACGATTCTTTGTACAATTTGCAACCAT
*
24517149 GGAATCCATAAAAAGAAATTTCATCTCTCAAGCTCCAATACTTATTGCATCCTCAAACTATGCTT
66 GGAATCCATAAAAA-AAATTTCATCTCTCAAGCTCCAATACTAATTGCATCCTCAAACTATGCTT
24517214 ATTGGAAAGCTCAAAATCAAGGCTTTCATAATG
130 ATTGGAAAGCTCAAAATCAAGGCTTTCATAATG
24517247 CTAGTTGATG
Statistics
Matches: 143, Mismatches: 18, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
162 67 0.47
163 56 0.39
164 20 0.14
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (163 bp):
CAATTAGTATCAAAATGAGCTTCAAGAGTTAATTAAAGACGATTCTTTGTACAATTTGCAACCAT
GGAATCCATAAAAAAAATTTCATCTCTCAAGCTCCAATACTAATTGCATCCTCAAACTATGCTTA
TTGGAAAGCTCAAAATCAAGGCTTTCATAATGA
Found at i:24522864 original size:20 final size:19
Alignment explanation
Indices: 24522825--24522869 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
24522815 TGAAATTTGT
***
24522825 AATTTAAATAAAATTTTAA
1 AATTTAAATAAAAACATAA
24522844 ATATTTAAATAAAAACATAA
1 A-ATTTAAATAAAAACATAA
24522864 AATTTA
1 AATTTA
24522870 GAAGTCAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (19 bp):
AATTTAAATAAAAACATAA
Found at i:24525703 original size:21 final size:22
Alignment explanation
Indices: 24525674--24525720 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
24525664 CAGAAGGAGT
*
24525674 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
24525696 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
24525717 GAGT
1 GAGT
24525721 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:24527807 original size:19 final size:19
Alignment explanation
Indices: 24527785--24527822 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
24527775 CATTAAATAG
24527785 TATTATCATTGTCAAATTA
1 TATTATCATTGTCAAATTA
24527804 TATTATCATTGTCAAATTA
1 TATTATCATTGTCAAATTA
24527823 GGACTTCATT
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:0.37, C:0.11, G:0.05, T:0.47
Consensus pattern (19 bp):
TATTATCATTGTCAAATTA
Found at i:24527831 original size:19 final size:19
Alignment explanation
Indices: 24527788--24527832 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
24527778 TAAATAGTAT
* *
24527788 TATCATTGTCAAATTATAT
1 TATCATTGTCAAATTAGAC
24527807 TATCATTGTCAAATTAGGAC
1 TATCATTGTCAAATTA-GAC
24527827 T-TCATT
1 TATCATT
24527833 TCCAAGGACA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 21 0.91
20 2 0.09
ACGTcount: A:0.33, C:0.13, G:0.09, T:0.44
Consensus pattern (19 bp):
TATCATTGTCAAATTAGAC
Found at i:24532611 original size:27 final size:28
Alignment explanation
Indices: 24532581--24532634 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
24532571 GATCCAACAG
* * *
24532581 ATTAATAATAAGTAATATTAT-TTAATT
1 ATTAATAACAAATAAAATTATATTAATT
24532608 ATTAATAACAAATAAAATTATATTAAT
1 ATTAATAACAAATAAAATTATATTAAT
24532635 CATATTTCTG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 18 0.78
28 5 0.22
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (28 bp):
ATTAATAACAAATAAAATTATATTAATT
Found at i:24539925 original size:19 final size:18
Alignment explanation
Indices: 24539888--24539927 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
24539878 TTTATATATA
**
24539888 TAATTATATTATTGCTCT
1 TAATTATATTATTAATCT
24539906 TAATATATATTATTAATCT
1 TAAT-TATATTATTAATCT
24539925 TAA
1 TAA
24539928 CCTCAATCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.38, C:0.07, G:0.03, T:0.53
Consensus pattern (18 bp):
TAATTATATTATTAATCT
Found at i:24542789 original size:146 final size:146
Alignment explanation
Indices: 24542533--24542825 Score: 541
Period size: 146 Copynumber: 2.0 Consensus size: 146
24542523 TATACACTTT
*
24542533 GGACAATTAACTTTTATCATACTTTATAACCAATACTTTGAAGTTGAATAATCTTCTTCACAAAG
1 GGACAATTAACTTTTACCATACTTTATAACCAATACTTTGAAGTTGAATAATCTTCTTCACAAAG
24542598 ACCTTTGAACTTGTTACTCAGAAGGGGAAAAGATTAACAATAATTCATCTACTTAAAAGCTCCTT
66 ACCTTTGAACTTGTTACTCAGAAGGGGAAAAGATTAACAATAATTCATCTACTTAAAAGCTCCTT
*
24542663 CAACTTTGTACACAGA
131 CAACGTTGTACACAGA
* *
24542679 GGACAATTAACTTTTACCTTACTTTATAACCAATACTTTGAAGTTGAATAATCTTCTTCATAAAG
1 GGACAATTAACTTTTACCATACTTTATAACCAATACTTTGAAGTTGAATAATCTTCTTCACAAAG
*
24542744 ACCTTTTAACTTGTTACTCAGAAGGGGAAAAGATTAACAATAATTCATCTACTTAAAAGCTCCTT
66 ACCTTTGAACTTGTTACTCAGAAGGGGAAAAGATTAACAATAATTCATCTACTTAAAAGCTCCTT
24542809 CAACGTTGTACACAGA
131 CAACGTTGTACACAGA
24542825 G
1 G
24542826 AACCAATCAA
Statistics
Matches: 142, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
146 142 1.00
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (146 bp):
GGACAATTAACTTTTACCATACTTTATAACCAATACTTTGAAGTTGAATAATCTTCTTCACAAAG
ACCTTTGAACTTGTTACTCAGAAGGGGAAAAGATTAACAATAATTCATCTACTTAAAAGCTCCTT
CAACGTTGTACACAGA
Found at i:24544842 original size:59 final size:59
Alignment explanation
Indices: 24544729--24544893 Score: 224
Period size: 59 Copynumber: 2.8 Consensus size: 59
24544719 AATGGCCGGC
* * * *
24544729 ACCATTGACAGGCCAACATCAAAAAATTATTTTTTTTTAAAAAACACGTATTTTGGTGCCG
1 ACCATTGACAGGCCAGCACCAAAAAA--ATTTTTTTTTAAAAAACTCATATTTTGGTGCCG
* *
24544790 GCCATTGACAGGCCAGCA-CAAAAAAATTTATTTTTTTAAAAACTCATATTTTGGTGCCG
1 ACCATTGACAGGCCAGCACCAAAAAAATTT-TTTTTTAAAAAACTCATATTTTGGTGCCG
* *
24544849 ACCATTGACAGGCCAGCACCAAATAAATTTTTTTTAAAAAAACTC
1 ACCATTGACAGGCCAGCACCAAAAAAATTTTTTTTTAAAAAACTC
24544894 GTTGTAGGGC
Statistics
Matches: 93, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
58 4 0.04
59 56 0.60
60 17 0.18
61 16 0.17
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.31
Consensus pattern (59 bp):
ACCATTGACAGGCCAGCACCAAAAAAATTTTTTTTTAAAAAACTCATATTTTGGTGCCG
Found at i:24558755 original size:177 final size:177
Alignment explanation
Indices: 24558445--24559200 Score: 989
Period size: 177 Copynumber: 4.3 Consensus size: 177
24558435 ATTATAGATT
** * *
24558445 TTATCTCCATGTATCGACTATGGAACAGATCTTAGCCACCAGCCTTATCTCTCTAAGATAGCAAG
1 TTATCTCCATGTATCGGTTATGGAGCAGATTTTAGCCACCAGCCTTATCTCTCTAAGATAGCAAG
* * *
24558510 AGAGCAGGTTGAAGATACAAGTTTTATCTTCCTGAAGTTGCAGGAACCAGACTGAAAATTACAGA
66 AGAGCAGGTTGAAGATACAAGTCTTATCTTCCTGAAGTTGCAGGAAGCAGACTGGAAATTACAGA
* *
24558575 TCTTATCTCCATGTACCGGTTATGGAGCAGATCAGAAATGGCGAGTC
131 TCTTATCTCCATGTATCGGCTATGGAGCAGATCAGAAATGGCGAGTC
* *
24558622 TTATCTCTATGTATCGGTTATGGAGCAGATTTTAGTCACCAGCCTTATCTCTCTAAGATAGCAAG
1 TTATCTCCATGTATCGGTTATGGAGCAGATTTTAGCCACCAGCCTTATCTCTCTAAGATAGCAAG
* *
24558687 AGAGTAGGTTGAAGATACAAGTCTTATCTTCCTGAAGTTGCAGGAAGCAGACTGGAAATTATAGA
66 AGAGCAGGTTGAAGATACAAGTCTTATCTTCCTGAAGTTGCAGGAAGCAGACTGGAAATTACAGA
24558752 TCTTATCTCCATGTATCGGCTATGGAGCAGATCAGAAATGGCGAGTC
131 TCTTATCTCCATGTATCGGCTATGGAGCAGATCAGAAATGGCGAGTC
* * * * * *
24558799 TTATCTCTATGTATCGGTTATGG-GACAAATTTTAGCCATCAGCCTTATCTCTCTGAGGTAACAA
1 TTATCTCCATGTATCGGTTATGGAG-CAGATTTTAGCCACCAGCCTTATCTCTCTAAGATAGCAA
* * * * ** *
24558863 GAGAGCAGGTTAAAGATATAAGTCTTATCTTCCTAAAGTTGTAGGAAGCAGGTTGTAAATTAC-G
65 GAGAGCAGGTTGAAGATACAAGTCTTATCTTCCTGAAGTTGCAGGAAGCAGACTGGAAATTACAG
* * *
24558927 AATCTTATCTTCATGTATCGGCTATGGAGCAGATC-GAAAATAGCGAATC
130 -ATCTTATCTCCATGTATCGGCTATGGAGCAGATCAG-AAATGGCGAGTC
* * * * * * *
24558976 TTATCTCCATGTATTGGTTATGGAGTAGATTTTAGCCACCAGTCTTATCTTTTTGAGGTAGCAAG
1 TTATCTCCATGTATCGGTTATGGAGCAGATTTTAGCCACCAGCCTTATCTCTCTAAGATAGCAAG
* * *
24559041 AGAGCAAGTTGAAGATACAAGTCTTATCTTCCTGAAGTTGTAAGAAGCAGACTGGAAATTACAGA
66 AGAGCAGGTTGAAGATACAAGTCTTATCTTCCTGAAGTTGCAGGAAGCAGACTGGAAATTACAGA
* *
24559106 TCTTA--TCC-----T--GCTATAGAGCAGGTCAGAAATGGCGAGTC
131 TCTTATCTCCATGTATCGGCTATGGAGCAGATCAGAAATGGCGAGTC
* **
24559144 TTATCTCCATGTATCGGCTACAGAGCAGATTTTAGCCACC-GACCTTATCTCTCTAAG
1 TTATCTCCATGTATCGGTTATGGAGCAGATTTTAGCCACCAG-CCTTATCTCTCTAAG
24559201 GTAGTAGTGG
Statistics
Matches: 510, Mismatches: 62, Indels: 23
0.86 0.10 0.04
Matches are distributed among these distances:
167 1 0.00
168 69 0.14
169 1 0.00
170 1 0.00
175 2 0.00
176 3 0.01
177 431 0.85
178 2 0.00
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.30
Consensus pattern (177 bp):
TTATCTCCATGTATCGGTTATGGAGCAGATTTTAGCCACCAGCCTTATCTCTCTAAGATAGCAAG
AGAGCAGGTTGAAGATACAAGTCTTATCTTCCTGAAGTTGCAGGAAGCAGACTGGAAATTACAGA
TCTTATCTCCATGTATCGGCTATGGAGCAGATCAGAAATGGCGAGTC
Done.