Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold114
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: 3219552
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Warning! 36736 characters in sequence are not A, C, G, or T
File 1 of 13
Found at i:675 original size:25 final size:24
Alignment explanation
Indices: 642--738 Score: 79
Period size: 25 Copynumber: 3.8 Consensus size: 24
632 ATAAACAAAT
*
642 AAATGAAAACAAAAAAAAAATTAAA
1 AAATTAAAA-AAAAAAAAAATTAAA
*
667 AAATTAAAAAAAATAATAAA-TAATA
1 AAATTAAAAAAAA-AAAAAATTAA-A
* * *
692 AAATTGAACAAAAAAATAAACTAAA
1 AAATT-AAAAAAAAAAAAAATTAAA
*
717 AAGACTTAAAAAAAGAAAAAAT
1 AA-A-TTAAAAAAAAAAAAAAT
739 CTAACATTTC
Statistics
Matches: 59, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
24 7 0.12
25 28 0.47
26 22 0.37
27 2 0.03
ACGTcount: A:0.75, C:0.04, G:0.04, T:0.16
Consensus pattern (24 bp):
AAATTAAAAAAAAAAAAAATTAAA
Found at i:3970 original size:36 final size:36
Alignment explanation
Indices: 3922--3994 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
3912 TGAAGAGAAC
3922 TATGTTTATTTTTACTTCTAGAATTGCTAGAGGTAA
1 TATGTTTATTTTTACTTCTAGAATTGCTAGAGGTAA
*
3958 TATGTTTGTTTTTACTTCTAGAATTGCTAGAGGTAA
1 TATGTTTATTTTTACTTCTAGAATTGCTAGAGGTAA
3994 T
1 T
3995 GTGATCTTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.26, C:0.08, G:0.18, T:0.48
Consensus pattern (36 bp):
TATGTTTATTTTTACTTCTAGAATTGCTAGAGGTAA
Found at i:13149 original size:27 final size:27
Alignment explanation
Indices: 13118--13176 Score: 109
Period size: 27 Copynumber: 2.2 Consensus size: 27
13108 TCAAGAATGT
13118 CTGAATAATTCTATATCTATAATGACA
1 CTGAATAATTCTATATCTATAATGACA
13145 CTGAATAATTCTATATCTATAATGACA
1 CTGAATAATTCTATATCTATAATGACA
*
13172 ATGAA
1 CTGAA
13177 CAATGAACAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.42, C:0.14, G:0.08, T:0.36
Consensus pattern (27 bp):
CTGAATAATTCTATATCTATAATGACA
Found at i:17579 original size:228 final size:229
Alignment explanation
Indices: 17160--17856 Score: 1047
Period size: 228 Copynumber: 3.0 Consensus size: 229
17150 GCAAAACCCA
* * *
17160 TTGCTTCATTGTCTACCACTTGGCCTATTTAACAAACTACAAGAAGGCAAGCAGAATGCATTATA
1 TTGCTTCATTGTCTTCCACTTGGCCTATCTAAC---C-ACAAGAAGGCAAGCAGAATACATTATA
17225 AAAAAGAAACCTTTTAAAATTAAAAT-AAAACAGAAATCCGGAACACCAAGGCCAAATCCAGCAC
62 AAAAAGAAACCTTTTAAAATTAAAATAAAAAC-GAAATCCGGAACACCAAGGCCAAATCCAGCAC
* * * *
17289 CTTGCCTACTCACTCTAAATCAATTGGCTTAATAAAAAGAATTGCTTGGAAATGGACGAATCATT
126 CTTGCCTACTTACTCTAAATCAATTGGGTTCATAAAAAGAATAGCTTGGAAATGGACGAATCATT
17354 CAAAAAAACTCTTTCACCAGTATCCTTTCTAGAACTGGT
191 CAAAAAAACTCTTTCACCAGTATCCTTTCTAGAACTGGT
* *
17393 TTGCTTCATTGTCTTCCACTTGGCCTATCTAACCACAAGGAGGCAAGCAGAATACATTACAAAAA
1 TTGCTTCATTGTCTTCCACTTGGCCTATCTAACCACAAGAAGGCAAGCAGAATACATTATAAAAA
17458 AGAAACCTTTTAAAATTAAAATAAAAACGAAATCCGGAACACCAAGGCC-AATCCAGCACCTTGC
66 AGAAACCTTTTAAAATTAAAATAAAAACGAAATCCGGAACACCAAGGCCAAATCCAGCACCTTGC
*
17522 CTACTTACTCTAAATCAATTGGGTTCATAAAAAGAATAGCTTGGAAATGGACGAATCATTCCAAA
131 CTACTTACTCTAAATCAATTGGGTTCATAAAAAGAATAGCTTGGAAATGGACGAATCATTCAAAA
*
17587 AAACTCTTTCACCAGCATCCTTTCTAGAACTGGT
196 AAACTCTTTCACCAGTATCCTTTCTAGAACTGGT
* * *
17621 TTGCTTCATTGTCATCCACTTGGCCTATCGGACAAACTACAAGAAGGCAAGCAGAATACATTATA
1 TTGCTTCATTGTCTTCCACTTGGCCTAT----CTAACCACAAGAAGGCAAGCAGAATACATTATA
* * *
17686 AAAAAGAAACCTTTTAAAATTAAAATAAAAAAGAAATCCAGAACACCAAGGCCAAATCCATCACC
62 AAAAAGAAACCTTTTAAAATTAAAATAAAAACGAAATCCGGAACACCAAGGCCAAATCCAGCACC
* * *
17751 TTGCTTACTTACTCTAAATCAATTGGGTTCATAAAAAGAACAGCTTGGAAAAATGGACAAATCAT
127 TTGCCTACTTACTCTAAATCAATTGGGTTCATAAAAAGAATAGCTTGG--AAATGGACGAATCAT
* ** * * *
17816 TCAGAAATCCTCTTTCACCAGTTTCCTTGCTAGAACGGGT
190 TCAAAAAAACTCTTTCACCAGTATCCTTTCTAGAACTGGT
17856 T
1 T
17857 GTCAATGCCT
Statistics
Matches: 426, Mismatches: 30, Indels: 14
0.91 0.06 0.03
Matches are distributed among these distances:
228 135 0.32
229 71 0.17
230 6 0.01
232 80 0.19
233 87 0.20
235 47 0.11
ACGTcount: A:0.39, C:0.22, G:0.14, T:0.25
Consensus pattern (229 bp):
TTGCTTCATTGTCTTCCACTTGGCCTATCTAACCACAAGAAGGCAAGCAGAATACATTATAAAAA
AGAAACCTTTTAAAATTAAAATAAAAACGAAATCCGGAACACCAAGGCCAAATCCAGCACCTTGC
CTACTTACTCTAAATCAATTGGGTTCATAAAAAGAATAGCTTGGAAATGGACGAATCATTCAAAA
AAACTCTTTCACCAGTATCCTTTCTAGAACTGGT
Found at i:25348 original size:12 final size:12
Alignment explanation
Indices: 25331--25355 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
25321 TCATATAGAC
25331 ATCTTTGACTAA
1 ATCTTTGACTAA
25343 ATCTTTGACTAA
1 ATCTTTGACTAA
25355 A
1 A
25356 GTATAAGGCT
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:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (12 bp):
ATCTTTGACTAA
Found at i:26422 original size:14 final size:14
Alignment explanation
Indices: 26387--26424 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
26377 AAATATTAAA
*
26387 ATATTTTTAATTAT
1 ATATTTTTATTTAT
26401 ATCA-TTTTATTTAT
1 AT-ATTTTTATTTAT
26415 ATATTTTTAT
1 ATATTTTTAT
26425 ATTTAAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
13 1 0.05
14 19 0.90
15 1 0.05
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (14 bp):
ATATTTTTATTTAT
Found at i:26480 original size:23 final size:23
Alignment explanation
Indices: 26453--26504 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
26443 CTTGTACTTC
*
26453 AAATTTATTTAAATATAAATAAA
1 AAATTTATTTAAATAAAAATAAA
** *
26476 AAA-TTATTTTGATAAAAATTAA
1 AAATTTATTTAAATAAAAATAAA
26498 AAATTTA
1 AAATTTA
26505 AAACAATTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
22 18 0.75
23 6 0.25
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (23 bp):
AAATTTATTTAAATAAAAATAAA
Found at i:27213 original size:16 final size:16
Alignment explanation
Indices: 27192--27232 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
27182 ATTTTAGATT
*
27192 TAAAAAAGTTGTTTAA
1 TAAAAAAATTGTTTAA
27208 TAAAAAAATTGTTTAA
1 TAAAAAAATTGTTTAA
27224 -AAAGAAAAT
1 TAAA-AAAAT
27233 GATATTTCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 3 0.13
16 20 0.87
ACGTcount: A:0.59, C:0.00, G:0.10, T:0.32
Consensus pattern (16 bp):
TAAAAAAATTGTTTAA
Found at i:58471 original size:229 final size:231
Alignment explanation
Indices: 58044--58741 Score: 1051
Period size: 232 Copynumber: 3.0 Consensus size: 231
58034 GCAAAATCCA
* *
58044 TTGCTTCATTGTCTACCACTTGGCCTATTTAACAAACTACAAGAAGGCAAGCAGAATGCATTATA
1 TTGCTTCATTGTCTTCCACTTGGCCTA--TAACAAACTACAAGAAGGCAAGCAGAATACATTATA
* * *
58109 AAAAAGAAACCTTTTAAAATTAAACTGAAAAGGAAATCCGGAACACCAAGGCCAAATCCAGCACC
64 AAAAAGAAACCTTTTAAAATTAAAATAAAAAAGAAATCCGGAACACCAAGGCCAAATCCAGCACC
* * *
58174 TTGCCTACTTACTCTAAATCAATTGGGTTCATAAAAGGAATTGCTTGAAAATGGACGAATCATTC
129 TTGCCTACTTACTCTAAATCAATTGGGTTCATAAAAAGAATAGCTTGGAAATGGACGAATCATTC
*
58239 AAAAAAAACTCTTTCACCAGTATCCTTTCTAGAACCGGT
194 -AAAAAAACTCTTTCACCAGTATCCTTTCTAGAACTGGT
* * *
58278 TTGCTTCATTGTCTTCCACTTGGCCTAT-A-TAACTACACGAAGGCAAGCAGAATACATTACAAA
1 TTGCTTCATTGTCTTCCACTTGGCCTATAACAAACTACAAGAAGGCAAGCAGAATACATTATAAA
* * *
58341 AAAGAAACCTTTCAAAATTAAAATAAAAACGAAATCCGGAGCACCAAGGCC-AATCCAGCACCTT
66 AAAGAAACCTTTTAAAATTAAAATAAAAAAGAAATCCGGAACACCAAGGCCAAATCCAGCACCTT
58405 GCCTACTTACTCTAAATCAATTGGGTTCATAAAAAGAATAGCTTGGAAATGGACGAATCATTCAA
131 GCCTACTTACTCTAAATCAATTGGGTTCATAAAAAGAATAGCTTGGAAATGGACGAATCATTCAA
* *
58470 AAAAACTCTTTCGCCAGCATCCTTTCTAGAACTGGT
196 AAAAACTCTTTCACCAGTATCCTTTCTAGAACTGGT
*
58506 TTGCTTCATTGTCTTCCGCTTGGCCTATCGAACAAACTACAAGAAGGCAAGCAGAATACATTATA
1 TTGCTTCATTGTCTTCCACTTGGCCTAT--AACAAACTACAAGAAGGCAAGCAGAATACATTATA
** * *
58571 AAAAAGAAACCTTTTAAAATTAAAATAAAAAAGAAATCCAAAACGCCAAGGCCAAATCCATCACC
64 AAAAAGAAACCTTTTAAAATTAAAATAAAAAAGAAATCCGGAACACCAAGGCCAAATCCAGCACC
* *
58636 TTGCCTACTTACTCTAAATCAATTGGGTTCATAAAAAGAACAGCTTGGAAAAATGGACAAATCAT
129 TTGCCTACTTACTCTAAATCAATTGGGTTCATAAAAAGAATAGCTTGG--AAATGGACGAATCAT
* ** * *
58701 TCAGAAATCCTCTTTCACCAGTTTCCATTCTAGAACTGGT
192 TCAAAAAAACTCTTTCACCAGTATCCTTTCTAGAACTGGT
58741 T
1 T
58742 ATCAATGCCT
Statistics
Matches: 421, Mismatches: 36, Indels: 13
0.90 0.08 0.03
Matches are distributed among these distances:
228 62 0.15
229 73 0.17
230 76 0.18
231 2 0.00
232 77 0.18
233 57 0.14
234 26 0.06
235 48 0.11
ACGTcount: A:0.39, C:0.22, G:0.14, T:0.26
Consensus pattern (231 bp):
TTGCTTCATTGTCTTCCACTTGGCCTATAACAAACTACAAGAAGGCAAGCAGAATACATTATAAA
AAAGAAACCTTTTAAAATTAAAATAAAAAAGAAATCCGGAACACCAAGGCCAAATCCAGCACCTT
GCCTACTTACTCTAAATCAATTGGGTTCATAAAAAGAATAGCTTGGAAATGGACGAATCATTCAA
AAAAACTCTTTCACCAGTATCCTTTCTAGAACTGGT
Found at i:60253 original size:9 final size:9
Alignment explanation
Indices: 60239--60265 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
60229 CAATAAGAAA
60239 AGCAGCAAC
1 AGCAGCAAC
60248 AGCAGCAAC
1 AGCAGCAAC
60257 AGCAGCAAC
1 AGCAGCAAC
60266 GACAAAAATA
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:0.44, C:0.33, G:0.22, T:0.00
Consensus pattern (9 bp):
AGCAGCAAC
Found at i:66292 original size:12 final size:12
Alignment explanation
Indices: 66275--66299 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
66265 TCATATAAAC
66275 ATCTTTGACTAA
1 ATCTTTGACTAA
66287 ATCTTTGACTAA
1 ATCTTTGACTAA
66299 A
1 A
66300 GTATAAGGCT
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:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (12 bp):
ATCTTTGACTAA
Found at i:66490 original size:3 final size:3
Alignment explanation
Indices: 66484--66509 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
66474 TTTTTTTTAA
66484 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
66510 ATGCTAATAT
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:67536 original size:29 final size:29
Alignment explanation
Indices: 67473--67529 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
67463 TATAAATAAA
*
67473 AAATTTGATAAAAATTAAAAATTTAAAAC
1 AAATTTGATAAAAATTAAAAATTAAAAAC
*
67502 AAATTTAGATAAAAATT-AAACTTAAAAA
1 AAATTT-GATAAAAATTAAAAATTAAAAA
67530 TATATTTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 15 0.60
30 10 0.40
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.30
Consensus pattern (29 bp):
AAATTTGATAAAAATTAAAAATTAAAAAC
Found at i:82327 original size:13 final size:13
Alignment explanation
Indices: 82309--82334 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
82299 AGGAAGACGA
82309 GAAAAGAAAAAAG
1 GAAAAGAAAAAAG
82322 GAAAAGAAAAAAG
1 GAAAAGAAAAAAG
82335 AAAGGTCTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (13 bp):
GAAAAGAAAAAAG
Found at i:83348 original size:19 final size:22
Alignment explanation
Indices: 83310--83351 Score: 63
Period size: 19 Copynumber: 2.0 Consensus size: 22
83300 CATACTAGGT
83310 AATATTAACATACAATAAACAA
1 AATATTAACATACAATAAACAA
83332 AATA-TAACAT-C-ATAAACAA
1 AATATTAACATACAATAAACAA
83351 A
1 A
83352 CAGTAAAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 9 0.45
20 1 0.05
21 6 0.30
22 4 0.20
ACGTcount: A:0.64, C:0.14, G:0.00, T:0.21
Consensus pattern (22 bp):
AATATTAACATACAATAAACAA
Found at i:84566 original size:2 final size:2
Alignment explanation
Indices: 84559--84588 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
84549 GAAATAGAAT
84559 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
84589 AAGAACATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:92524 original size:13 final size:13
Alignment explanation
Indices: 92506--92531 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
92496 TGTTGAAATT
92506 GAAAAAAAAAAAA
1 GAAAAAAAAAAAA
92519 GAAAAAAAAAAAA
1 GAAAAAAAAAAAA
92532 AAAGAAATGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (13 bp):
GAAAAAAAAAAAA
Found at i:92528 original size:16 final size:16
Alignment explanation
Indices: 92507--92538 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
92497 GTTGAAATTG
92507 AAAAAAAAAAAAGAAA
1 AAAAAAAAAAAAGAAA
92523 AAAAAAAAAAAAGAAA
1 AAAAAAAAAAAAGAAA
92539 TGATTCAGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.94, C:0.00, G:0.06, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAAAGAAA
Found at i:94056 original size:18 final size:19
Alignment explanation
Indices: 94029--94070 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
94019 AACCTTGAGA
* *
94029 AAAATTAAGTGAACC-AAG
1 AAAATCAAGTAAACCAAAG
94047 AAAATCAAGTAAACCAAAG
1 AAAATCAAGTAAACCAAAG
94066 AAAAT
1 AAAAT
94071 AAAGCATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.62, C:0.12, G:0.12, T:0.14
Consensus pattern (19 bp):
AAAATCAAGTAAACCAAAG
Found at i:95231 original size:229 final size:221
Alignment explanation
Indices: 94835--95289 Score: 608
Period size: 229 Copynumber: 2.0 Consensus size: 221
94825 GCAAAATCCA
* * *
94835 TTGCTTCATTGTCTGCCACTTGGCTTATCTAACAAACTACAAGAAGGCAAGCAGAATGCATTATA
1 TTGCTTCATTGTCTGCCACTTCGCCTATCT---AAACTACAAGAAGGCAAGCAGAATACATTATA
*
94900 AAAAAGAAACCTTTCAAAATTAAAATAAAAAAGAACCAAGGCCAAATCCAGCACCTTGCCTACTT
63 AAAAAGAAACCTTTCAAAATTAAAATAAAAAAGAACCAAGGCCAAACCCAGCACCTTGCCTACTT
* * *
94965 ACTCTAAATCAATTGGGTTCATAAAAAGAATAGCTTGG-AAATGGACGAATCATTCAAAAAAATT
128 ACTCTAAATCAATTGGGTTCATAAAAAGAACAGCTTGGAAAATGGACAAATCATTCAAAAAAACT
95029 CTTTCACCAGTATCCTTTCTAGAACTGGT
193 CTTTCACCAGTATCCTTTCTAGAACTGGT
* *
95058 TTGCTTCATTGTCTTCCACTTCGCCTATCT-AACTACCAGAAGGCAAGCAGAATACATTATAAAA
1 TTGCTTCATTGTCTGCCACTTCGCCTATCTAAACTACAAGAAGGCAAGCAGAATACATTATAAAA
* * *
95122 AAGAAAGCTTTTAAAATTAAAATAAAAAAGAAATCCAGAACACCAAGGCCAAACCCATCACCTTG
66 AAGAAACCTTTCAAAATTAAAAT----AA-AAA---AG-A-ACCAAGGCCAAACCCAGCACCTTG
* *
95187 CCTACTTACTCTAAATCAATTGGGTTCATAAAAAGAACAGCTTGGAAAAATGGACAAATCGTTCC
121 CCTACTTACTCTAAATCAATTGGGTTCATAAAAAGAACAGCTTGG-AAAATGGACAAATCATTCA
* * * *
95252 GAAAACCTCTTTCACCGGTTTCCTTTCTAGAACTGGT
185 AAAAAACTCTTTCACCAGTATCCTTTCTAGAACTGGT
95289 T
1 T
95290 GTCAATGCCT
Statistics
Matches: 202, Mismatches: 18, Indels: 16
0.86 0.08 0.07
Matches are distributed among these distances:
219 53 0.26
223 29 0.14
224 3 0.01
227 2 0.01
228 1 0.00
229 66 0.33
231 48 0.24
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.26
Consensus pattern (221 bp):
TTGCTTCATTGTCTGCCACTTCGCCTATCTAAACTACAAGAAGGCAAGCAGAATACATTATAAAA
AAGAAACCTTTCAAAATTAAAATAAAAAAGAACCAAGGCCAAACCCAGCACCTTGCCTACTTACT
CTAAATCAATTGGGTTCATAAAAAGAACAGCTTGGAAAATGGACAAATCATTCAAAAAAACTCTT
TCACCAGTATCCTTTCTAGAACTGGT
Found at i:105254 original size:21 final size:21
Alignment explanation
Indices: 105221--105264 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
105211 ATACTTACAA
** * *
105221 TTTTATATTTTATTATTCTAT
1 TTTTATAAATTATAATTATAT
105242 TTTTATAAATTATAATTATAT
1 TTTTATAAATTATAATTATAT
105263 TT
1 TT
105265 AAAATATTAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (21 bp):
TTTTATAAATTATAATTATAT
Found at i:105275 original size:20 final size:20
Alignment explanation
Indices: 105250--105289 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
105240 ATTTTTATAA
*
105250 ATTATA-ATTATATTTAAAAT
1 ATTATATATT-TATATAAAAT
105270 ATTATATATTTATATAAAAT
1 ATTATATATTTATATAAAAT
105290 TTAATATACT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATTATATATTTATATAAAAT
Found at i:105357 original size:28 final size:29
Alignment explanation
Indices: 105326--105406 Score: 87
Period size: 28 Copynumber: 2.8 Consensus size: 29
105316 ATTTTTAATA
105326 TTTTAATATTATATAATATGTAAATTA-T
1 TTTTAATATTATATAATATGTAAATTACT
* * * *
105354 TTTTAATATAATATTATATTTTAATTACT
1 TTTTAATATTATATAATATGTAAATTACT
105383 TTTT-ATATCATATATAAT-TGTAAA
1 TTTTAATAT--TATATAATATGTAAA
105407 AATATCTGCA
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
28 27 0.64
29 9 0.21
30 6 0.14
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (29 bp):
TTTTAATATTATATAATATGTAAATTACT
Found at i:105924 original size:20 final size:22
Alignment explanation
Indices: 105899--105941 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
105889 TCATTAAAAT
105899 TAATTATTCA-TT-ATATTTAA
1 TAATTATTCATTTAATATTTAA
*
105919 TAATTATTTATTTAATATTTAA
1 TAATTATTCATTTAATATTTAA
105941 T
1 T
105942 TTTTTAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 9 0.45
21 2 0.10
22 9 0.45
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (22 bp):
TAATTATTCATTTAATATTTAA
Found at i:105932 original size:15 final size:16
Alignment explanation
Indices: 105898--105949 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 16
105888 ATCATTAAAA
* *
105898 TTAATTATTCATTATAT
1 TTAATAATTAATT-TAT
105915 TTAATAATT-ATTTAT
1 TTAATAATTAATTTAT
*
105930 TTAATATTTAATTT-T
1 TTAATAATTAATTTAT
105945 TTAAT
1 TTAAT
105950 TAAACTAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
15 17 0.53
16 7 0.22
17 8 0.25
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (16 bp):
TTAATAATTAATTTAT
Found at i:106763 original size:20 final size:20
Alignment explanation
Indices: 106740--106798 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
106730 ATATATTTAG
*
106740 AATTAAATTTAAATAAAATA
1 AATTTAATTTAAATAAAATA
*
106760 AATTTTA-TTAAATTAAAATA
1 AATTTAATTTAAA-TAAAATA
* *
106780 AATTTGATTAAAATAAAAT
1 AATTTAATTTAAATAAAAT
106799 TTATGTTAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 5 0.15
20 24 0.73
21 4 0.12
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (20 bp):
AATTTAATTTAAATAAAATA
Found at i:115916 original size:2 final size:2
Alignment explanation
Indices: 115909--115947 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
115899 GATATACTAT
115909 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
115948 TATTTTTTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:117981 original size:121 final size:121
Alignment explanation
Indices: 117767--118009 Score: 486
Period size: 121 Copynumber: 2.0 Consensus size: 121
117757 CCACCCACAA
117767 TCCGAACTTTTGCCTGGGCTTAGATTTGGTTATGTATGTATGTATGTGAGAATCTAGTCTTTTGT
1 TCCGAACTTTTGCCTGGGCTTAGATTTGGTTATGTATGTATGTATGTGAGAATCTAGTCTTTTGT
117832 ACTGGCAAATGGAAGATGGTGCTGTATAATGCAGTATTTATATGTCTATGTTCTGT
66 ACTGGCAAATGGAAGATGGTGCTGTATAATGCAGTATTTATATGTCTATGTTCTGT
117888 TCCGAACTTTTGCCTGGGCTTAGATTTGGTTATGTATGTATGTATGTGAGAATCTAGTCTTTTGT
1 TCCGAACTTTTGCCTGGGCTTAGATTTGGTTATGTATGTATGTATGTGAGAATCTAGTCTTTTGT
117953 ACTGGCAAATGGAAGATGGTGCTGTATAATGCAGTATTTATATGTCTATGTTCTGT
66 ACTGGCAAATGGAAGATGGTGCTGTATAATGCAGTATTTATATGTCTATGTTCTGT
118009 T
1 T
118010 ACCTTGTATG
Statistics
Matches: 122, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
121 122 1.00
ACGTcount: A:0.22, C:0.12, G:0.25, T:0.42
Consensus pattern (121 bp):
TCCGAACTTTTGCCTGGGCTTAGATTTGGTTATGTATGTATGTATGTGAGAATCTAGTCTTTTGT
ACTGGCAAATGGAAGATGGTGCTGTATAATGCAGTATTTATATGTCTATGTTCTGT
Found at i:122689 original size:14 final size:14
Alignment explanation
Indices: 122667--122700 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
122657 AAAGAAAATG
*
122667 TTTGTTTTTGGTTT
1 TTTGCTTTTGGTTT
122681 TTTGCTTTTGGTTT
1 TTTGCTTTTGGTTT
122695 TTTGCT
1 TTTGCT
122701 AAATCAAGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.00, C:0.06, G:0.21, T:0.74
Consensus pattern (14 bp):
TTTGCTTTTGGTTT
Found at i:126348 original size:21 final size:21
Alignment explanation
Indices: 126314--126353 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
126304 TAATTTTATT
126314 TAAATTTAATTATAAAATATA
1 TAAATTTAATTATAAAATATA
126335 TAAATATTAA-TATAAAATA
1 TAAAT-TTAATTATAAAATA
126354 ATTTTTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATTTAATTATAAAATATA
Found at i:126376 original size:13 final size:14
Alignment explanation
Indices: 126332--126404 Score: 52
Period size: 13 Copynumber: 5.6 Consensus size: 14
126322 ATTATAAAAT
126332 ATATAAAT-ATT-A
1 ATATAAATAATTAA
126344 ATATAAAATAATT--
1 ATAT-AAATAATTAA
* *
126357 TTTTAAA-AATTAA
1 ATATAAATAATTAA
*
126370 TTATAAATAA-TAA
1 ATATAAATAATTAA
126383 ATATAAATAATTTAA
1 ATATAAATAA-TTAA
126398 A-ATAAAT
1 ATATAAAT
126405 TTTAATAAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
11 4 0.08
12 7 0.14
13 24 0.48
14 11 0.22
15 4 0.08
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
ATATAAATAATTAA
Found at i:126399 original size:48 final size:50
Alignment explanation
Indices: 126290--126417 Score: 158
Period size: 48 Copynumber: 2.6 Consensus size: 50
126280 AACTGATATT
* *
126290 TAATAATTTAAAAATAATTTTATTTAAATTTAATTATAAAATATATAAATA
1 TAATAATTT-AAAATAATTTTATTAAAAATTAATTATAAAATATATAAATA
*
126341 T--TAATATAAAATAATTTT-TTAAAAATTAATTAT-AAATA-ATAAATA
1 TAATAATTTAAAATAATTTTATTAAAAATTAATTATAAAATATATAAATA
*
126386 TAAATAATTTAAAATAAATTTTAATAAAAATT
1 T-AATAATTTAAAAT-AATTTTATTAAAAATT
126418 TAAAATTTTT
Statistics
Matches: 67, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
45 8 0.12
46 5 0.07
47 13 0.19
48 21 0.31
49 11 0.16
50 8 0.12
51 1 0.01
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (50 bp):
TAATAATTTAAAATAATTTTATTAAAAATTAATTATAAAATATATAAATA
Found at i:126405 original size:38 final size:38
Alignment explanation
Indices: 126333--126405 Score: 87
Period size: 38 Copynumber: 1.9 Consensus size: 38
126323 TTATAAAATA
* **
126333 TATAAATATTAATATAAAATAATTTTTTAAAAATTAAT
1 TATAAATATAAATATAAAATAATTTTAAAAAAATTAAT
126371 TATAAATAATAAATAT-AAATAA-TTTAAAATAAATT
1 TATAAAT-ATAAATATAAAATAATTTTAAAA-AAATT
126406 TTAATAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
37 5 0.17
38 18 0.60
39 7 0.23
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (38 bp):
TATAAATATAAATATAAAATAATTTTAAAAAAATTAAT
Found at i:126732 original size:19 final size:20
Alignment explanation
Indices: 126698--126736 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
126688 TTTAAAATTT
126698 TATAAAAATAAATAATTAAA
1 TATAAAAATAAATAATTAAA
*
126718 TATAAAAA-AATTAATTAAA
1 TATAAAAATAAATAATTAAA
126737 AAAGGTGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (20 bp):
TATAAAAATAAATAATTAAA
Found at i:127213 original size:15 final size:13
Alignment explanation
Indices: 127185--127223 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 13
127175 ATATTTAATA
127185 AATTTAAAATTTT
1 AATTTAAAATTTT
127198 AATTTATAATATTTT
1 AATTTA-AA-ATTTT
*
127213 ATTTTAAAATT
1 AATTTAAAATT
127224 AAGTTATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
13 9 0.39
14 4 0.17
15 10 0.43
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
AATTTAAAATTTT
Found at i:127472 original size:2 final size:2
Alignment explanation
Indices: 127467--127508 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
127457 CAAAAAAATA
127467 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
127509 CAAAGGTCAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:129181 original size:3 final size:3
Alignment explanation
Indices: 129173--129206 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
129163 CCATGCATCA
*
129173 AAT AAT AAT AAT AAT AAT AAT AAC AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
129207 CAATTTTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:130150 original size:3 final size:3
Alignment explanation
Indices: 130142--130174 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
130132 AAACGAACAT
130142 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
130175 GCATCATATA
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:132550 original size:57 final size:56
Alignment explanation
Indices: 132475--132590 Score: 178
Period size: 57 Copynumber: 2.1 Consensus size: 56
132465 TTCCCTTACT
*
132475 TTTGACATAAAAATAAATACTGAATTAATTCATTATTATTACGATCATGCAGTTAAA
1 TTTGACATAAAAATAAATACTGAATTAATTCATTATT-TTACGATCATGCAGTCAAA
* * * *
132532 TTTGGCATAAAAATAAATATTGAATTAATTCATTATTTTATGATCATGTAGTCAAA
1 TTTGACATAAAAATAAATACTGAATTAATTCATTATTTTACGATCATGCAGTCAAA
132588 TTT
1 TTT
132591 CATCCAAAAT
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
56 19 0.35
57 35 0.65
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (56 bp):
TTTGACATAAAAATAAATACTGAATTAATTCATTATTTTACGATCATGCAGTCAAA
Found at i:132782 original size:2 final size:2
Alignment explanation
Indices: 132775--132802 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
132765 CCACACCCTC
132775 CT 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 CT
132803 TGCAGTTGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:133363 original size:26 final size:27
Alignment explanation
Indices: 133307--133364 Score: 64
Period size: 26 Copynumber: 2.1 Consensus size: 27
133297 TTATTATGTA
** *
133307 ATTTTTACTTTTAATATTTAAATTTTTT
1 ATTTTTAC-TTTAATATTTAAATAATAT
*
133335 ATTTTTA-TTTAATTTTTAAATAATAT
1 ATTTTTACTTTAATATTTAAATAATAT
133361 ATTT
1 ATTT
133365 AAAAGATTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 19 0.73
28 7 0.27
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.66
Consensus pattern (27 bp):
ATTTTTACTTTAATATTTAAATAATAT
Found at i:133856 original size:12 final size:12
Alignment explanation
Indices: 133832--133871 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
133822 TTTAAATAAA
*
133832 TAATTAAATATT
1 TAATTAAAAATT
133844 TAATTAAAAATT
1 TAATTAAAAATT
*
133856 TATTTAAAAAATT
1 TAATT-AAAAATT
133869 TAA
1 TAA
133872 AAAAAAAGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
12 15 0.62
13 9 0.38
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
TAATTAAAAATT
Found at i:134546 original size:23 final size:24
Alignment explanation
Indices: 134518--134581 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 24
134508 AGTTCAGCTT
*
134518 ATTTTTATTATATAATATGTAT-TA
1 ATTTTCATTATATAATAT-TATGTA
134542 ATTTTACATT-TATATATATTATGTA
1 ATTTT-CATTATATA-ATATTATGTA
*
134567 ATTTTCATCATATAA
1 ATTTTCATTATATAA
134582 AAGATAATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
24 16 0.47
25 18 0.53
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.55
Consensus pattern (24 bp):
ATTTTCATTATATAATATTATGTA
Found at i:135163 original size:24 final size:26
Alignment explanation
Indices: 135100--135163 Score: 73
Period size: 24 Copynumber: 2.6 Consensus size: 26
135090 TAAGTATGAC
135100 AATATAAAATTATTAAAATACGAAAT
1 AATATAAAATTATTAAAATACGAAAT
** *
135126 AA-ATAAAATT-TTAAAAT-TTATAT
1 AATATAAAATTATTAAAATACGAAAT
135149 AATAT-AAATTATTAA
1 AATATAAAATTATTAA
135164 TATATCAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
23 10 0.30
24 13 0.39
25 8 0.24
26 2 0.06
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (26 bp):
AATATAAAATTATTAAAATACGAAAT
Found at i:135932 original size:23 final size:22
Alignment explanation
Indices: 135884--135932 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
135874 TTAATAAAAA
* * * *
135884 ATAATTTTATTAAAATTTAATT
1 ATAATTATATAAAAAATTAATC
135906 ATAATTATATAAAAAATTATATC
1 ATAATTATATAAAAAATTA-ATC
135929 ATAA
1 ATAA
135933 ATTTTTAATA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
ATAATTATATAAAAAATTAATC
Found at i:136414 original size:16 final size:16
Alignment explanation
Indices: 136390--136436 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 16
136380 AAACAAAAAA
*
136390 TATATATATATATATT
1 TATAAATATATATATT
136406 TATAAATATATA-ATT
1 TATAAATATATATATT
*
136421 TA-AAAAATATAT-TT
1 TATAAATATATATATT
136435 TA
1 TA
136437 ACTTATAACT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 12 0.43
15 5 0.18
16 11 0.39
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TATAAATATATATATT
Found at i:138236 original size:17 final size:17
Alignment explanation
Indices: 138206--138241 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
138196 AATCAAAATA
*
138206 ATCGTAATTGTAATTAT
1 ATCGTAATTCTAATTAT
*
138223 ATCGTTATTCTAATTAT
1 ATCGTAATTCTAATTAT
138240 AT
1 AT
138242 AGAGAATAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.33, C:0.08, G:0.08, T:0.50
Consensus pattern (17 bp):
ATCGTAATTCTAATTAT
Found at i:144496 original size:21 final size:21
Alignment explanation
Indices: 144459--144498 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
144449 AGGTGAGTGG
*
144459 TTAAAAAAATATAAATTATGA
1 TTAAAAAAAAATAAATTATGA
144480 TTAAAAATAAAAT-AATTAT
1 TTAAAAA-AAAATAAATTAT
144499 TAATGTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (21 bp):
TTAAAAAAAAATAAATTATGA
Found at i:144500 original size:18 final size:19
Alignment explanation
Indices: 144463--144501 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
144453 GAGTGGTTAA
*
144463 AAAAATATAAATTATGATT
1 AAAAATATAAATAATGATT
*
144482 AAAAATA-AAATAATTATT
1 AAAAATATAAATAATGATT
144500 AA
1 AA
144502 TGTTTTAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (19 bp):
AAAAATATAAATAATGATT
Found at i:146839 original size:2 final size:2
Alignment explanation
Indices: 146832--146859 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
146822 ATATTCTCAA
146832 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
146860 TATGCAGCTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:148176 original size:2 final size:2
Alignment explanation
Indices: 148169--148199 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
148159 TTAAAGGTGT
148169 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
148200 GTTACATAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:153050 original size:27 final size:26
Alignment explanation
Indices: 153019--153078 Score: 111
Period size: 27 Copynumber: 2.3 Consensus size: 26
153009 GAAATTTTGG
153019 CAAAATTAACTATTTCAAATTGAATTT
1 CAAAATTAACTATTTCAAATTGAA-TT
153046 CAAAATTAACTATTTCAAATTGAATT
1 CAAAATTAACTATTTCAAATTGAATT
153072 CAAAATT
1 CAAAATT
153079 GGCTGCACAG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 9 0.27
27 24 0.73
ACGTcount: A:0.47, C:0.12, G:0.03, T:0.38
Consensus pattern (26 bp):
CAAAATTAACTATTTCAAATTGAATT
Found at i:153062 original size:15 final size:15
Alignment explanation
Indices: 153019--153064 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
153009 GAAATTTTGG
153019 CAAAATTAACTATTT
1 CAAAATTAACTATTT
*
153034 C-AAATTGA--ATTT
1 CAAAATTAACTATTT
153046 CAAAATTAACTATTT
1 CAAAATTAACTATTT
153061 CAAA
1 CAAA
153065 TTGAATTCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
12 5 0.19
13 6 0.23
14 6 0.23
15 9 0.35
ACGTcount: A:0.48, C:0.13, G:0.02, T:0.37
Consensus pattern (15 bp):
CAAAATTAACTATTT
Found at i:153079 original size:12 final size:13
Alignment explanation
Indices: 153030--153079 Score: 52
Period size: 12 Copynumber: 3.9 Consensus size: 13
153020 AAAATTAACT
153030 ATTTC-AAATTGA
1 ATTTCAAAATTGA
*
153042 ATTTCAAAATTAA
1 ATTTCAAAATTGA
153055 CTATTTC-AAATTGA
1 --ATTTCAAAATTGA
153069 A-TTCAAAATTG
1 ATTTCAAAATTG
153080 GCTGCACAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
11 3 0.09
12 12 0.38
13 6 0.19
14 6 0.19
15 5 0.16
ACGTcount: A:0.44, C:0.10, G:0.06, T:0.40
Consensus pattern (13 bp):
ATTTCAAAATTGA
Found at i:157729 original size:9 final size:9
Alignment explanation
Indices: 157715--157747 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
157705 TTTCTCTCTT
*
157715 TCTGCTATC
1 TCTGCTGTC
157724 TCTGCTGTC
1 TCTGCTGTC
157733 TCTGCTGTC
1 TCTGCTGTC
157742 TCTGCT
1 TCTGCT
157748 TGAGCCTTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.03, C:0.33, G:0.18, T:0.45
Consensus pattern (9 bp):
TCTGCTGTC
Found at i:157844 original size:27 final size:26
Alignment explanation
Indices: 157806--157857 Score: 86
Period size: 27 Copynumber: 2.0 Consensus size: 26
157796 TGCAACTTTT
157806 ACTATTTCAAATTGAATTTCAAAATTA
1 ACTATTTCAAATTGAA-TTCAAAATTA
*
157833 ACTATTTTAAATTGAATTCAAAATT
1 ACTATTTCAAATTGAATTCAAAATT
157858 GGCTGCACTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 9 0.38
27 15 0.62
ACGTcount: A:0.44, C:0.10, G:0.04, T:0.42
Consensus pattern (26 bp):
ACTATTTCAAATTGAATTCAAAATTA
Found at i:158869 original size:12 final size:14
Alignment explanation
Indices: 158842--158873 Score: 50
Period size: 12 Copynumber: 2.4 Consensus size: 14
158832 TATTTTTATT
158842 TAAATATAATTAAA
1 TAAATATAATTAAA
158856 TAAATAT-A-TAAA
1 TAAATATAATTAAA
158868 TAAATA
1 TAAATA
158874 ATATTTAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 10 0.56
13 1 0.06
14 7 0.39
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
TAAATATAATTAAA
Found at i:162102 original size:2 final size:2
Alignment explanation
Indices: 162095--162123 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
162085 ATCTACGTAG
162095 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
162124 AAAAAGTCTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:165438 original size:3 final size:3
Alignment explanation
Indices: 165430--165469 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
165420 CACTTAAATA
*
165430 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
165470 GTTTCTGTCG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:165788 original size:2 final size:2
Alignment explanation
Indices: 165781--165807 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
165771 CTAATCACCA
165781 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 A
165808 CATACGCACA
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:166462 original size:15 final size:15
Alignment explanation
Indices: 166442--166473 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
166432 GATATTTAAT
*
166442 ATTTTTATAAATATA
1 ATTTTTAAAAATATA
166457 ATTTTTAAAAATATA
1 ATTTTTAAAAATATA
166472 AT
1 AT
166474 AATATCTTTA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTTTTAAAAATATA
Found at i:168192 original size:28 final size:29
Alignment explanation
Indices: 168138--168192 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 29
168128 TAATTTATAT
* ***
168138 TTTAAAAATTATTTTTATTATTTAAATGA
1 TTTAAAAAATATTTTTATTAAAAAAATGA
168167 TTTAAAAAATATTTTT-TTAAAAAAAT
1 TTTAAAAAATATTTTTATTAAAAAAAT
168193 TAATTTAATA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
28 7 0.32
29 15 0.68
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (29 bp):
TTTAAAAAATATTTTTATTAAAAAAATGA
Found at i:169950 original size:3 final size:3
Alignment explanation
Indices: 169944--169980 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
169934 AAAAAAAAAA
169944 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
169981 GTTCTAACTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:173890 original size:23 final size:23
Alignment explanation
Indices: 173864--173909 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
173854 TTCTACCCTT
173864 AATTTTATTAGATAATGCATGGG
1 AATTTTATTAGATAATGCATGGG
173887 AATTTTATTAGATAATGCATGGG
1 AATTTTATTAGATAATGCATGGG
173910 GGATGTTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.04, G:0.22, T:0.39
Consensus pattern (23 bp):
AATTTTATTAGATAATGCATGGG
Found at i:178351 original size:31 final size:30
Alignment explanation
Indices: 178316--178378 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 30
178306 GTTCAGTTTC
178316 TTTTTTT--TTTTTAATTTCTTTTTTAATG
1 TTTTTTTGGTTTTTAATTTCTTTTTTAATG
* * *
178344 CTTTTTTTGGTTTTTCATTTTTTTTTTCATG
1 -TTTTTTTGGTTTTTAATTTCTTTTTTAATG
178375 TTTT
1 TTTT
178379 CACTCTTTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
29 7 0.24
30 4 0.14
31 18 0.62
ACGTcount: A:0.10, C:0.06, G:0.06, T:0.78
Consensus pattern (30 bp):
TTTTTTTGGTTTTTAATTTCTTTTTTAATG
Found at i:183163 original size:2 final size:2
Alignment explanation
Indices: 183150--183193 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
183140 ATGTACAACA
*
183150 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
183192 AT
1 AT
183194 GATGAGATGG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:183982 original size:26 final size:26
Alignment explanation
Indices: 183930--183982 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
183920 GAGTTTTAAT
183930 TTAAATAAAAGTAATTAAATTTAAAA
1 TTAAATAAAAGTAATTAAATTTAAAA
* *
183956 TTAAATATAA-TATTTAAATTTATAAA
1 TTAAATAAAAGTAATTAAATTTA-AAA
183982 T
1 T
183983 GTTGAAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 11 0.46
26 13 0.54
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (26 bp):
TTAAATAAAAGTAATTAAATTTAAAA
Found at i:184277 original size:3 final size:3
Alignment explanation
Indices: 184269--184302 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
184259 ATTGATATTC
*
184269 TAT TAT TAT TAT TAC TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
184303 CATACTTGGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:184727 original size:3 final size:3
Alignment explanation
Indices: 184721--184754 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
184711 TTATACAATA
*
184721 ATT ATT ATT ATT ATT ATT ATT GTT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
184755 AAATAAACTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:201402 original size:3 final size:3
Alignment explanation
Indices: 201394--201439 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
201384 CAAACCCAGA
201394 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
201440 ATTTTTTGCC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:205994 original size:17 final size:17
Alignment explanation
Indices: 205972--206028 Score: 64
Period size: 17 Copynumber: 3.3 Consensus size: 17
205962 AAATTTTTAA
205972 ATATTATTTTTTTATTT
1 ATATTATTTTTTTATTT
*
205989 ATATTAATTTTTTATGTT
1 ATATTATTTTTTTAT-TT
206007 ATAATT-TTTATTTTATTT
1 AT-ATTATTT-TTTTATTT
206025 -TATT
1 ATATT
206029 TTTGATATCA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
16 3 0.09
17 15 0.43
18 8 0.23
19 9 0.26
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (17 bp):
ATATTATTTTTTTATTT
Found at i:206395 original size:21 final size:21
Alignment explanation
Indices: 206370--206416 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
206360 GTGTTTTGTG
206370 ATATAAATATG-GTAAAAATA
1 ATATAAATATGTGTAAAAATA
*
206390 AT-TATAATATGTGTAAATATA
1 ATATA-AATATGTGTAAAAATA
206411 ATATAA
1 ATATAA
206417 TATAAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
19 2 0.09
20 8 0.35
21 11 0.48
22 2 0.09
ACGTcount: A:0.55, C:0.00, G:0.09, T:0.36
Consensus pattern (21 bp):
ATATAAATATGTGTAAAAATA
Found at i:206400 original size:20 final size:20
Alignment explanation
Indices: 206370--206419 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
206360 GTGTTTTGTG
206370 ATATAAATATG-GTAAAAATA
1 ATAT-AATATGTGTAAAAATA
*
206390 ATTATAATATGTGTAAATATA
1 A-TATAATATGTGTAAAAATA
206411 ATATAATAT
1 ATATAATAT
206420 AAAAAAATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 15 0.56
21 12 0.44
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (20 bp):
ATATAATATGTGTAAAAATA
Found at i:206530 original size:20 final size:22
Alignment explanation
Indices: 206498--206557 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 22
206488 TATTAAATTT
* *
206498 ATATAAATATATAATATTT-TAA
1 ATATAGAT-TATAATATTTAAAA
206520 ATATA-ATTATAAATATTTAAAA
1 ATATAGATTAT-AATATTTAAAA
206542 ATATATGATTATAATA
1 ATATA-GATTATAATA
206558 CGAATATAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
20 3 0.09
21 9 0.27
22 12 0.36
23 4 0.12
24 5 0.15
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
ATATAGATTATAATATTTAAAA
Found at i:206530 original size:22 final size:22
Alignment explanation
Indices: 206471--206546 Score: 64
Period size: 22 Copynumber: 3.3 Consensus size: 22
206461 AAATTTTTAT
*
206471 AATATGAATCATAAATATATTAAA
1 AATATAAAT-ATAAATAT-TTAAA
* *
206495 TTTATATAAATATATAATATTT-TA
1 --AATATAAATATA-AATATTTAAA
*
206519 AATATAATTATAAATATTTAAA
1 AATATAAATATAAATATTTAAA
206541 AATATA
1 AATATA
206547 TGATTATAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
21 7 0.17
22 17 0.40
24 1 0.02
25 5 0.12
26 12 0.29
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (22 bp):
AATATAAATATAAATATTTAAA
Found at i:206547 original size:24 final size:24
Alignment explanation
Indices: 206472--206555 Score: 66
Period size: 24 Copynumber: 3.5 Consensus size: 24
206462 AATTTTTATA
* **
206472 ATATGAATCATAAATATATTAAATTT
1 ATAT-AATTATAAATAT-TTAAAAAT
* *
206498 ATATAAATATATAATATTT-T-AA-
1 ATATAATTATA-AATATTTAAAAAT
206520 ATATAATTATAAATATTTAAAAAT
1 ATATAATTATAAATATTTAAAAAT
*
206544 ATATGATTATAA
1 ATATAATTATAA
206556 TACGAATATA
Statistics
Matches: 46, Mismatches: 8, Indels: 10
0.72 0.12 0.16
Matches are distributed among these distances:
21 7 0.15
22 10 0.22
23 2 0.04
24 11 0.24
25 7 0.15
26 9 0.20
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.43
Consensus pattern (24 bp):
ATATAATTATAAATATTTAAAAAT
Found at i:211276 original size:2 final size:2
Alignment explanation
Indices: 211271--211296 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
211261 AAATACACAC
211271 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
211297 TCAACATACT
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:214268 original size:14 final size:14
Alignment explanation
Indices: 214240--214283 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
214230 GATAATATCA
214240 TTAAA-TTTAAAAT
1 TTAAATTTTAAAAT
*
214253 TTAAATTTTAATAT
1 TTAAATTTTAAAAT
*
214267 TTATAATTTTTAAAT
1 TTA-AATTTTAAAAT
214282 TT
1 TT
214284 TTTTTATTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
13 5 0.19
14 10 0.38
15 11 0.42
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTAAATTTTAAAAT
Found at i:214282 original size:23 final size:23
Alignment explanation
Indices: 214252--214301 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
214242 AAATTTAAAA
214252 TTTAAATTTTA-ATATTTATAATT
1 TTTAAATTTTATATA-TTATAATT
* *
214275 TTTAAATTTTTTTTATTATAATT
1 TTTAAATTTTATATATTATAATT
214298 TTTA
1 TTTA
214302 TTAAAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 22 0.92
24 2 0.08
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (23 bp):
TTTAAATTTTATATATTATAATT
Found at i:214985 original size:3 final size:3
Alignment explanation
Indices: 214977--215009 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
214967 GTTCAATTTA
214977 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
215010 CAGAATTCCT
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):
AAT
Found at i:216915 original size:36 final size:36
Alignment explanation
Indices: 216860--216936 Score: 129
Period size: 36 Copynumber: 2.2 Consensus size: 36
216850 TGCTTGCTGG
216860 TGTC-TTTTTTTTACCGTGTTCAGCAGTTTTGTAGT
1 TGTCTTTTTTTTTACCGTGTTCAGCAGTTTTGTAGT
*
216895 TGTCTTTTTTTTTACTGTGTTCAGCAGTTTTGTAGT
1 TGTCTTTTTTTTTACCGTGTTCAGCAGTTTTGTAGT
*
216931 TATCTT
1 TGTCTT
216937 AGTGCATATT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
35 4 0.10
36 35 0.90
ACGTcount: A:0.12, C:0.13, G:0.18, T:0.57
Consensus pattern (36 bp):
TGTCTTTTTTTTTACCGTGTTCAGCAGTTTTGTAGT
Found at i:220087 original size:25 final size:25
Alignment explanation
Indices: 220006--220087 Score: 62
Period size: 25 Copynumber: 3.2 Consensus size: 25
219996 ATTAACAAGA
*
220006 GGAAGAGTTTAATATATAAATGCAG
1 GGAAGAGTTTAATATGTAAATGCAG
* *
220031 GGAATGAGCTATGTTAT-TGGATAAACG-A-
1 GGAA-GAG-T-T-TAATAT-G-TAAATGCAG
220059 GGAAGAGTTTAATATGTAAATGCAG
1 GGAAGAGTTTAATATGTAAATGCAG
220084 GGAA
1 GGAA
220088 TGAAATTTAG
Statistics
Matches: 43, Mismatches: 5, Indels: 18
0.65 0.08 0.27
Matches are distributed among these distances:
23 5 0.12
24 5 0.12
25 10 0.23
26 4 0.09
27 4 0.09
28 6 0.14
29 4 0.09
30 5 0.12
ACGTcount: A:0.40, C:0.05, G:0.28, T:0.27
Consensus pattern (25 bp):
GGAAGAGTTTAATATGTAAATGCAG
Found at i:227063 original size:21 final size:21
Alignment explanation
Indices: 227039--227080 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
227029 ATTTTTATTT
*
227039 TAAATAT-TTATATTTTTTTAA
1 TAAATATATT-TATTATTTTAA
227060 TAAATATATTTATTATTTTAA
1 TAAATATATTTATTATTTTAA
227081 ATGTAACACT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TAAATATATTTATTATTTTAA
Found at i:230886 original size:11 final size:11
Alignment explanation
Indices: 230844--230908 Score: 51
Period size: 13 Copynumber: 5.5 Consensus size: 11
230834 GTATATAAAT
230844 TTATATTTTTA
1 TTATATTTTTA
*
230855 TATCATATTTATA
1 T-T-ATATTTTTA
*
230868 TAAT-TTTTTA
1 TTATATTTTTA
*
230878 TTATATTTTAA
1 TTATATTTTTA
230889 TTATTTATTTTATA
1 TTA--TATTTT-TA
230903 TTATAT
1 TTATAT
230909 GTATATCATG
Statistics
Matches: 42, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
10 8 0.19
11 11 0.26
12 4 0.10
13 15 0.36
14 4 0.10
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (11 bp):
TTATATTTTTA
Found at i:230894 original size:21 final size:22
Alignment explanation
Indices: 230847--230904 Score: 59
Period size: 21 Copynumber: 2.7 Consensus size: 22
230837 TATAAATTTA
*
230847 TATTTTTATATCATA-TTTATAT
1 TATTTTT-TATTATATTTTATAT
*
230869 AATTTTTTATTATATTTTA-AT
1 TATTTTTTATTATATTTTATAT
*
230890 TATTTATT-TTATATT
1 TATTTTTTATTATATT
230905 ATATGTATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
20 7 0.23
21 14 0.45
22 10 0.32
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (22 bp):
TATTTTTTATTATATTTTATAT
Found at i:237104 original size:17 final size:16
Alignment explanation
Indices: 237071--237101 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
237061 TTTAAATTTA
237071 ATAAAAAATATTAAAT
1 ATAAAAAATATTAAAT
*
237087 ATAAAAAATTTTAAA
1 ATAAAAAATATTAAA
237102 ATAGTAAATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
ATAAAAAATATTAAAT
Found at i:240535 original size:6 final size:6
Alignment explanation
Indices: 240524--240553 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
240514 TGTTCTTAAT
240524 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA
1 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA
240554 TGTTGAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
ATAAAA
Found at i:240617 original size:15 final size:15
Alignment explanation
Indices: 240591--240637 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
240581 GTTAAGAAAC
240591 TTATAA-TAATAAAT
1 TTATAATTAATAAAT
240605 TTATAATTAATAAA-
1 TTATAATTAATAAAT
240619 -TATAATATAAGTAAAT
1 TTATAAT-TAA-TAAAT
240635 TTA
1 TTA
240638 AAAATTTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
13 6 0.21
14 9 0.32
15 11 0.39
17 2 0.07
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (15 bp):
TTATAATTAATAAAT
Found at i:241060 original size:24 final size:23
Alignment explanation
Indices: 241018--241105 Score: 81
Period size: 24 Copynumber: 3.8 Consensus size: 23
241008 GATTTTTAAT
241018 TTTATAAATATTAAATAAACATA
1 TTTATAAATATTAAATAAACATA
* **
241041 TTTATAAATATATAATTAAATTTA
1 TTTATAAATAT-TAAATAAACATA
**
241065 TTTATAAATAATT-AA-AAGTATA
1 TTTATAAAT-ATTAAATAAACATA
* *
241087 TTCATAAATAATAAATAAA
1 TTTATAAATATTAAATAAA
241106 TAAATATATT
Statistics
Matches: 52, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
21 2 0.04
22 15 0.29
23 14 0.27
24 19 0.37
25 2 0.04
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.41
Consensus pattern (23 bp):
TTTATAAATATTAAATAAACATA
Found at i:241063 original size:20 final size:20
Alignment explanation
Indices: 241040--241080 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
241030 AAATAAACAT
*
241040 ATTTATAAATATATAATTAA
1 ATTTATAAATAAATAATTAA
**
241060 ATTTATTTATAAATAATTAA
1 ATTTATAAATAAATAATTAA
241080 A
1 A
241081 AGTATATTCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
ATTTATAAATAAATAATTAA
Found at i:243800 original size:3 final size:3
Alignment explanation
Indices: 243792--243834 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
243782 TCTTCCAGAA
*
243792 AAT AAT AAT AAT AAT AAT TAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
243835 TTATTATTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:252873 original size:30 final size:29
Alignment explanation
Indices: 252839--252914 Score: 91
Period size: 30 Copynumber: 2.6 Consensus size: 29
252829 AGATACATGT
*
252839 GCTGCATTTACATGAACTACAGCTGCAC-GA
1 GCTGCATTTGCATGAACTACAG-T-CACAGA
**
252869 GCTGCACGTGCATGAACTACAGTCACATGA
1 GCTGCATTTGCATGAACTACAGTCACA-GA
252899 GCTGCATTTGCATGAA
1 GCTGCATTTGCATGAA
252915 TTGCAATCAG
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
28 3 0.08
29 1 0.03
30 35 0.90
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.24
Consensus pattern (29 bp):
GCTGCATTTGCATGAACTACAGTCACAGA
Found at i:255966 original size:2 final size:2
Alignment explanation
Indices: 255961--255997 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
255951 AAAGAGAGTT
*
255961 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TT TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
255998 TTTTTTAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (2 bp):
TC
Found at i:256728 original size:20 final size:20
Alignment explanation
Indices: 256703--256758 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
256693 ATAATTATTT
256703 TATTTTTTTATGATTATTAA
1 TATTTTTTTATGATTATTAA
** *
256723 TATTTTTTTAAAAATATTAA
1 TATTTTTTTATGATTATTAA
256743 -ATATTTTTTATGATTA
1 TAT-TTTTTTATGATTA
256759 AATTACTAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
19 2 0.07
20 27 0.93
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.61
Consensus pattern (20 bp):
TATTTTTTTATGATTATTAA
Found at i:258709 original size:7 final size:7
Alignment explanation
Indices: 258697--258745 Score: 57
Period size: 7 Copynumber: 7.1 Consensus size: 7
258687 GTTATTTAGT
258697 TATGATA
1 TATGATA
258704 TATGATA
1 TATGATA
*
258711 T-CGATA
1 TATGATA
258717 TATGATA
1 TATGATA
*
258724 T-CGATA
1 TATGATA
258730 TATGATA
1 TATGATA
258737 TCATGATA
1 T-ATGATA
258745 T
1 T
258746 GTCATGTTGG
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
6 10 0.29
7 18 0.51
8 7 0.20
ACGTcount: A:0.39, C:0.06, G:0.14, T:0.41
Consensus pattern (7 bp):
TATGATA
Found at i:258746 original size:13 final size:13
Alignment explanation
Indices: 258700--258738 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
258690 ATTTAGTTAT
258700 GATATATGATATC
1 GATATATGATATC
258713 GATATATGATATC
1 GATATATGATATC
258726 GATATATGATATC
1 GATATATGATATC
258739 ATGATATGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.38
Consensus pattern (13 bp):
GATATATGATATC
Found at i:258906 original size:28 final size:25
Alignment explanation
Indices: 258866--258930 Score: 76
Period size: 28 Copynumber: 2.5 Consensus size: 25
258856 CGTTTGTTGT
* *
258866 AATATTTTATATTATAATTATATTTAAA
1 AATATTTTATATT-TAAATAAATTT--A
*
258894 AATATTTTATATTTAAATAAATTTT
1 AATATTTTATATTTAAATAAATTTA
258919 AATATTTTATAT
1 AATATTTTATAT
258931 AATTATTAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
25 12 0.35
27 9 0.26
28 13 0.38
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (25 bp):
AATATTTTATATTTAAATAAATTTA
Found at i:258925 original size:18 final size:17
Alignment explanation
Indices: 258883--258925 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
258873 TATATTATAA
258883 TTATATTTAAAAATATT
1 TTATATTTAAAAATATT
258900 TTATATTTAAATAA-ATT
1 TTATATTTAAA-AATATT
258917 TTAATATTT
1 TT-ATATTT
258926 TATATAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 16 0.67
18 8 0.33
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTATATTTAAAAATATT
Found at i:266869 original size:21 final size:21
Alignment explanation
Indices: 266843--266886 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
266833 CGATTTGGAC
*
266843 AATTTATTTAAATTAAAAATT
1 AATTTAATTAAATTAAAAATT
* *
266864 AATTTAATTAATTTTAAAATT
1 AATTTAATTAAATTAAAAATT
266885 AA
1 AA
266887 AATTGGTTGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
AATTTAATTAAATTAAAAATT
Found at i:267059 original size:23 final size:24
Alignment explanation
Indices: 267024--267068 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
267014 CAAACTAATC
**
267024 TTTTTTTTTTTGTTTTT-TTAAAA
1 TTTTTTTAATTGTTTTTGTTAAAA
267047 TTTTTTTAATTGTTTTTGTTAA
1 TTTTTTTAATTGTTTTTGTTAA
267069 GGTGAAGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.18, C:0.00, G:0.07, T:0.76
Consensus pattern (24 bp):
TTTTTTTAATTGTTTTTGTTAAAA
Found at i:267197 original size:28 final size:29
Alignment explanation
Indices: 267143--267199 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
267133 TGGGTTACCA
* *
267143 AATTTTATTCAATTTACTTTTTTTTTTTT
1 AATTTTATTCAAGTTACTTTTTATTTTTT
267172 AATTTTA-TCAAGTTA-TTTTATATTTTTT
1 AATTTTATTCAAGTTACTTTT-TATTTTTT
267200 TATTAAACTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 4 0.16
28 14 0.56
29 7 0.28
ACGTcount: A:0.25, C:0.05, G:0.02, T:0.68
Consensus pattern (29 bp):
AATTTTATTCAAGTTACTTTTTATTTTTT
Found at i:267197 original size:29 final size:29
Alignment explanation
Indices: 267143--267201 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 29
267133 TGGGTTACCA
*
267143 AATTTTATTCAATTTACTTTTTTTTTTTT
1 AATTTTATTCAAGTTACTTTTTTTTTTTT
267172 AATTTTA-TCAAGTTA-TTTTATATTTTTTT
1 AATTTTATTCAAGTTACTTTT-T-TTTTTTT
267201 A
1 A
267202 TTAAACTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
27 4 0.15
28 8 0.30
29 15 0.56
ACGTcount: A:0.25, C:0.05, G:0.02, T:0.68
Consensus pattern (29 bp):
AATTTTATTCAAGTTACTTTTTTTTTTTT
Found at i:267266 original size:12 final size:12
Alignment explanation
Indices: 267237--267266 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
267227 TGAATTTAAG
*
267237 TTTATATAGATT
1 TTTATTTAGATT
267249 TTTATTTAGATT
1 TTTATTTAGATT
267261 TTTATT
1 TTTATT
267267 AAATTTGAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.67
Consensus pattern (12 bp):
TTTATTTAGATT
Found at i:267348 original size:38 final size:39
Alignment explanation
Indices: 267294--267373 Score: 101
Period size: 39 Copynumber: 2.1 Consensus size: 39
267284 TATATAGATT
* * *
267294 TTTAATTTGTATTAAATAGA-TTTAATTTTTAAGTTTAA
1 TTTAATTTGTATTAAATAGATTTTAAATATTAAATTTAA
*
267332 TTTATATTT-TATTAAATATATTTTAAATATTAAATTTAA
1 TTTA-ATTTGTATTAAATAGATTTTAAATATTAAATTTAA
267371 TTT
1 TTT
267374 TTTTAATTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
38 14 0.39
39 22 0.61
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (39 bp):
TTTAATTTGTATTAAATAGATTTTAAATATTAAATTTAA
Found at i:270791 original size:14 final size:14
Alignment explanation
Indices: 270772--270808 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
270762 GCTCTGGTTT
270772 CTCTGTTTTCCAAA
1 CTCTGTTTTCCAAA
*
270786 CTCTGTTTTCTAAA
1 CTCTGTTTTCCAAA
270800 CTCTGTTTT
1 CTCTGTTTT
270809 TATATAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.16, C:0.24, G:0.08, T:0.51
Consensus pattern (14 bp):
CTCTGTTTTCCAAA
Found at i:271316 original size:30 final size:30
Alignment explanation
Indices: 271293--271421 Score: 112
Period size: 28 Copynumber: 4.5 Consensus size: 30
271283 TAAGGGTTTG
271293 TTTGAGTATAAATTAAAAATTAAGAATTTA
1 TTTGAGTATAAATTAAAAATTAAGAATTTA
* * *
271323 TTT-AGTTAAAAATTAAATATTAAGAGTTTA
1 TTTGAG-TATAAATTAAAAATTAAGAATTTA
* *
271353 TTTAAGTGT-AA-TAAAAATTAA-AGATTTA
1 TTTGAGTATAAATTAAAAATTAAGA-ATTTA
* *
271381 TTTGAGTAT-AA-TAAAATTATAAAAATTTA
1 TTTGAGTATAAATTAAAAAT-TAAGAATTTA
271410 TTT-AG-ATAAATT
1 TTTGAGTATAAATT
271422 TATAAAGTTT
Statistics
Matches: 82, Mismatches: 10, Indels: 15
0.77 0.09 0.14
Matches are distributed among these distances:
27 3 0.04
28 32 0.39
29 16 0.20
30 29 0.35
31 2 0.02
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.42
Consensus pattern (30 bp):
TTTGAGTATAAATTAAAAATTAAGAATTTA
Found at i:271759 original size:18 final size:18
Alignment explanation
Indices: 271738--271773 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
271728 ATCAAGAAAA
* *
271738 AAAATTAATTTTAAATTT
1 AAAATTAAATTAAAATTT
271756 AAAATTAAATTAAAATTT
1 AAAATTAAATTAAAATTT
271774 TAATATATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AAAATTAAATTAAAATTT
Found at i:271816 original size:26 final size:25
Alignment explanation
Indices: 271759--271816 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 25
271749 TAAATTTAAA
271759 ATTAAATTAAAATTTTAATATATTT
1 ATTAAATTAAAATTTTAATATATTT
* *
271784 ATATAAATTTAAATTATT-ATTTATTT
1 AT-TAAATTAAAATT-TTAATATATTT
271810 CATTAAA
1 -ATTAAA
271817 AATTTATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
25 2 0.07
26 22 0.79
27 4 0.14
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (25 bp):
ATTAAATTAAAATTTTAATATATTT
Found at i:271885 original size:19 final size:19
Alignment explanation
Indices: 271857--271904 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
271847 TATAATTAAA
271857 TTTAAA-TAAAAATATTAT
1 TTTAAATTAAAAATATTAT
* *
271875 TTTAATTTAAAATTATTAT
1 TTTAAATTAAAAATATTAT
271894 TTTAAATTAAA
1 TTTAAATTAAA
271905 TCAAAATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 5 0.19
19 21 0.81
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TTTAAATTAAAAATATTAT
Found at i:271889 original size:50 final size:48
Alignment explanation
Indices: 271813--271932 Score: 145
Period size: 50 Copynumber: 2.4 Consensus size: 48
271803 TTTATTTCAT
**
271813 TAAAAATTTATTTT-ATATTAATAATTATATATTTTATAATTAAATTTAAA
1 TAAAAATTTATTTTAAT-TTAATAATTAT-TATTTTA-AATTAAATCAAAA
271863 TAAAAATATTATTTTAATTTAA-AATTATTATTTTAAATTAAATCAAAA
1 TAAAAAT-TTATTTTAATTTAATAATTATTATTTTAAATTAAATCAAAA
271911 TAAAAAATTTTAATTTTAATTT
1 T-AAAAA-TTT-ATTTTAATTT
271933 TAATTTCATC
Statistics
Matches: 63, Mismatches: 2, Indels: 10
0.84 0.03 0.13
Matches are distributed among these distances:
48 12 0.19
49 14 0.22
50 24 0.38
51 11 0.17
52 2 0.03
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (48 bp):
TAAAAATTTATTTTAATTTAATAATTATTATTTTAAATTAAATCAAAA
Found at i:271910 original size:24 final size:23
Alignment explanation
Indices: 271852--271911 Score: 65
Period size: 19 Copynumber: 2.7 Consensus size: 23
271842 TATTTTATAA
*
271852 TTAAATTTAAATAAAAATATTATT
1 TTAAA-TTAAATAAAATTATTATT
271876 TT-AATT---TAAAATTATTATT
1 TTAAATTAAATAAAATTATTATT
271895 TTAAATTAAATCAAAAT
1 TTAAATTAAAT-AAAAT
271912 AAAAAATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 10
0.73 0.02 0.24
Matches are distributed among these distances:
19 14 0.47
20 4 0.13
22 2 0.07
23 3 0.10
24 7 0.23
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (23 bp):
TTAAATTAAATAAAATTATTATT
Found at i:278999 original size:29 final size:29
Alignment explanation
Indices: 278963--279020 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
278953 GAGTGTTAAC
* *
278963 GTGATTAGAGAGATAGCTGTGAATAACAA
1 GTGATTAGAGAGATAACTGTCAATAACAA
*
278992 GTGATTAGAGGGATAACTGTCAATAACAA
1 GTGATTAGAGAGATAACTGTCAATAACAA
279021 AATTATAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.41, C:0.09, G:0.26, T:0.24
Consensus pattern (29 bp):
GTGATTAGAGAGATAACTGTCAATAACAA
Found at i:279897 original size:2 final size:2
Alignment explanation
Indices: 279892--279924 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
279882 ATATATATAT
*
279892 AG AG AG AG AG AG AG AG AG CG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
279925 TAGAAGCTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:280376 original size:23 final size:23
Alignment explanation
Indices: 280350--280411 Score: 67
Period size: 22 Copynumber: 2.8 Consensus size: 23
280340 GTTTATAATT
280350 ATATTAATATATTTAATTTCAAA
1 ATATTAATATATTTAATTTCAAA
*
280373 ATATT-ATAATATTT-ATTTTAAA
1 ATATTAAT-ATATTTAATTTCAAA
* *
280395 AT-TAAATATATTAAATT
1 ATATTAATATATTTAATT
280412 ATTATAAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
21 6 0.18
22 16 0.48
23 11 0.33
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (23 bp):
ATATTAATATATTTAATTTCAAA
Found at i:285388 original size:16 final size:16
Alignment explanation
Indices: 285367--285397 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
285357 TATTTTTTAT
285367 TATTTTATTAATAAAA
1 TATTTTATTAATAAAA
285383 TATTTTATTAATAAA
1 TATTTTATTAATAAA
285398 TTATATAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TATTTTATTAATAAAA
Found at i:285713 original size:7 final size:7
Alignment explanation
Indices: 285703--285728 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
285693 TTAATCTTAA
285703 ATTTTTT
1 ATTTTTT
285710 ATTTTTT
1 ATTTTTT
285717 ATTTTTT
1 ATTTTTT
285724 ATTTT
1 ATTTT
285729 ATTTATATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
ATTTTTT
Found at i:288695 original size:51 final size:50
Alignment explanation
Indices: 288616--288906 Score: 313
Period size: 51 Copynumber: 6.0 Consensus size: 50
288606 CAGAGGGGAG
* *
288616 TCATAAATAACGAAGAGGAACATCATCTGGATAAGACATCTTCTACTGATA
1 TCATAAATAATGAGGAGGAACATCATCTGGATAAGACA-CTTCTACTGATA
*
288667 TCGTAAATAA-GAGGGAGGAACATCATCT-G----G--A----TACTGATA
1 TCATAAATAATGA-GGAGGAACATCATCTGGATAAGACACTTCTACTGATA
* * * *
288706 TCATAAATAAAGAAGACGAAAATCATCTGGATAAGACACCTTCTACTGATA
1 TCATAAATAATGAGGAGGAACATCATCTGGATAAGACA-CTTCTACTGATA
* * *
288757 TCATAAATAATGTGGAGGAACATCATCTGGACAATACACCTTCTACTGATA
1 TCATAAATAATGAGGAGGAACATCATCTGGATAAGACA-CTTCTACTGATA
* *
288808 TCATAAATAATGAGGAGGAACATCATCTGGATAATACAC--CTACTGATG
1 TCATAAATAATGAGGAGGAACATCATCTGGATAAGACACTTCTACTGATA
* *
288856 TCATAAACAATGAAGAGGAACATCATCTGGATAAGACATCTTCTACTGATA
1 TCATAAATAATGAGGAGGAACATCATCTGGATAAGACA-CTTCTACTGATA
288907 CTGCCAACAG
Statistics
Matches: 203, Mismatches: 20, Indels: 34
0.79 0.08 0.13
Matches are distributed among these distances:
39 29 0.14
40 3 0.01
44 2 0.01
46 2 0.01
48 43 0.21
49 1 0.00
50 4 0.02
51 119 0.59
ACGTcount: A:0.41, C:0.17, G:0.17, T:0.25
Consensus pattern (50 bp):
TCATAAATAATGAGGAGGAACATCATCTGGATAAGACACTTCTACTGATA
Found at i:288702 original size:39 final size:39
Alignment explanation
Indices: 288659--288738 Score: 108
Period size: 39 Copynumber: 2.1 Consensus size: 39
288649 AGACATCTTC
* * * *
288659 TACTGATATCGTAAAT-AAGAGGGAGGAACATCATCTGGA
1 TACTGATATCATAAATAAAGA-AGACGAAAATCATCTGGA
288698 TACTGATATCATAAATAAAGAAGACGAAAATCATCTGGA
1 TACTGATATCATAAATAAAGAAGACGAAAATCATCTGGA
288737 TA
1 TA
288739 AGACACCTTC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
39 32 0.89
40 4 0.11
ACGTcount: A:0.44, C:0.12, G:0.20, T:0.24
Consensus pattern (39 bp):
TACTGATATCATAAATAAAGAAGACGAAAATCATCTGGA
Found at i:288774 original size:90 final size:90
Alignment explanation
Indices: 288616--288787 Score: 274
Period size: 90 Copynumber: 1.9 Consensus size: 90
288606 CAGAGGGGAG
* * * * *
288616 TCATAAATAACGAAGAGGAACATCATCTGGATAAGACATCTTCTACTGATATCGTAAATAAGAGG
1 TCATAAATAAAGAAGACGAAAATCATCTGGATAAGACACCTTCTACTGATATCATAAATAAGAGG
288681 GAGGAACATCATCTGGATACTGATA
66 GAGGAACATCATCTGGATACTGATA
*
288706 TCATAAATAAAGAAGACGAAAATCATCTGGATAAGACACCTTCTACTGATATCATAAATAATG-T
1 TCATAAATAAAGAAGACGAAAATCATCTGGATAAGACACCTTCTACTGATATCATAAATAA-GAG
288770 GGAGGAACATCATCTGGA
65 GGAGGAACATCATCTGGA
288788 CAATACACCT
Statistics
Matches: 75, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
90 74 0.99
91 1 0.01
ACGTcount: A:0.41, C:0.16, G:0.19, T:0.24
Consensus pattern (90 bp):
TCATAAATAAAGAAGACGAAAATCATCTGGATAAGACACCTTCTACTGATATCATAAATAAGAGG
GAGGAACATCATCTGGATACTGATA
Found at i:288899 original size:99 final size:101
Alignment explanation
Indices: 288698--288906 Score: 287
Period size: 99 Copynumber: 2.1 Consensus size: 101
288688 ATCATCTGGA
288698 TACTGATATCATAAATAAAGAAGACGAAAATCATCTGGATAAGACACCTTCTACTGATATCATAA
1 TACTGATATCATAAATAAAGAAGACGAAAATCATCTGGATAAGACACC-TCTACTGATATCATAA
* ** *
288763 ATAATGTGGAGGAACATCATCTGGACAATACACCTTC
65 ACAATGAAGAGGAACATCATCTGGACAAGACACCTTC
* * * * * *
288800 TACTGATATCATAAATAATGAGGAGGAACATCATCTGGATAATACA-C-CTACTGATGTCATAAA
1 TACTGATATCATAAATAAAGAAGACGAAAATCATCTGGATAAGACACCTCTACTGATATCATAAA
* *
288863 CAATGAAGAGGAACATCATCTGGATAAGACATCTTC
66 CAATGAAGAGGAACATCATCTGGACAAGACACCTTC
288899 TACTGATA
1 TACTGATA
288907 CTGCCAACAG
Statistics
Matches: 95, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
99 53 0.56
101 1 0.01
102 41 0.43
ACGTcount: A:0.41, C:0.18, G:0.16, T:0.26
Consensus pattern (101 bp):
TACTGATATCATAAATAAAGAAGACGAAAATCATCTGGATAAGACACCTCTACTGATATCATAAA
CAATGAAGAGGAACATCATCTGGACAAGACACCTTC
Done.