Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold224
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: 480342
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
File 2 of 3
Found at i:204180 original size:28 final size:31
Alignment explanation
Indices: 204128--204196 Score: 90
Period size: 28 Copynumber: 2.3 Consensus size: 31
204118 AAATTATTTA
*
204128 AATATAAAATATTTTCAAATGAATATTAAAAAT
1 AATAT-AAA-ATTTTCAAATGAATATAAAAAAT
204161 AAT-TAAAATTTT-AAAT-AATATAAAAAAT
1 AATATAAAATTTTCAAATGAATATAAAAAAT
204189 AATATAAA
1 AATATAAA
204197 TATAATTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
28 14 0.41
29 8 0.24
30 5 0.15
31 3 0.09
32 1 0.03
33 3 0.09
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (31 bp):
AATATAAAATTTTCAAATGAATATAAAAAAT
Found at i:204230 original size:34 final size:34
Alignment explanation
Indices: 204154--204243 Score: 94
Period size: 34 Copynumber: 2.6 Consensus size: 34
204144 AAATGAATAT
*
204154 TAAAAATAATTA-AAATTTTAAATAATATAAAAA
1 TAAAAATAAATATAAATTTTAAATAATATAAAAA
* * * *
204187 -ATAATATAAATATAATTTTTTATTAATATAAAAA
1 TA-AAAATAAATATAAATTTTAAATAATATAAAAA
*
204221 TAAAAATAAAAATAAATTATTAA
1 TAAAAATAAATATAAATT-TTAA
204244 TATTTTAAAT
Statistics
Matches: 44, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
32 1 0.02
33 8 0.18
34 31 0.70
35 4 0.09
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (34 bp):
TAAAAATAAATATAAATTTTAAATAATATAAAAA
Found at i:204236 original size:40 final size:40
Alignment explanation
Indices: 204157--204272 Score: 109
Period size: 40 Copynumber: 3.0 Consensus size: 40
204147 TGAATATTAA
* * * *
204157 AAATAATTAAAATTTTAAATA-AT-ATAAAAAAT-AATAT
1 AAATTATTAATATTTTAAATATATAAAAAAAAATAAAAAT
*
204194 AAA-TA-TAATTTTTTATTAATATA-AAAATAAAAATAAAAAT
1 AAATTATTAATATTTTA--AATATATAAAA-AAAAATAAAAAT
*
204234 AAATTATTAATATTTTAAATATATAAAAAATAATAAAAA
1 AAATTATTAATATTTTAAATATATAAAAAAAAATAAAAA
204273 ATAACACGAA
Statistics
Matches: 63, Mismatches: 7, Indels: 15
0.74 0.08 0.18
Matches are distributed among these distances:
35 8 0.13
36 1 0.02
37 7 0.11
38 3 0.05
39 6 0.10
40 23 0.37
41 6 0.10
42 9 0.14
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (40 bp):
AAATTATTAATATTTTAAATATATAAAAAAAAATAAAAAT
Found at i:204355 original size:29 final size:29
Alignment explanation
Indices: 204323--204382 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 29
204313 TCTCCTTTTT
*
204323 TCTTCCCTTCTGCTTCCTTTATCTTTCTC
1 TCTTCCCTTCTGCTTCCTTTATATTTCTC
* * ** *
204352 TCTTTCTTTCTTTTTCCTTTTTATTTCTC
1 TCTTCCCTTCTGCTTCCTTTATATTTCTC
204381 TC
1 TC
204383 CACCCGAAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.03, C:0.32, G:0.02, T:0.63
Consensus pattern (29 bp):
TCTTCCCTTCTGCTTCCTTTATATTTCTC
Found at i:213332 original size:51 final size:51
Alignment explanation
Indices: 213266--213381 Score: 187
Period size: 51 Copynumber: 2.3 Consensus size: 51
213256 TTTTACCCAG
*
213266 ATGTATCGATACATTCTGTCTTTTTACCTAGATGTATCGATACATTTAAAA
1 ATGTATCGATACATTCTATCTTTTTACCTAGATGTATCGATACATTTAAAA
* ***
213317 ATGTATCGATACATTCTATTTTTTTACCTAGATGTATCGATACATTTTTCA
1 ATGTATCGATACATTCTATCTTTTTACCTAGATGTATCGATACATTTAAAA
213368 ATGTATCGATACAT
1 ATGTATCGATACAT
213382 GTATGAATGT
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 60 1.00
ACGTcount: A:0.30, C:0.16, G:0.11, T:0.43
Consensus pattern (51 bp):
ATGTATCGATACATTCTATCTTTTTACCTAGATGTATCGATACATTTAAAA
Found at i:213373 original size:20 final size:20
Alignment explanation
Indices: 213348--213418 Score: 88
Period size: 20 Copynumber: 3.5 Consensus size: 20
213338 TTTTACCTAG
*
213348 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTAA
* * *
213368 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTAA
*
213388 ATGTATCGATACATTCTTAA
1 ATGTATCGATACATTTTTAA
*
213408 ATGTATTGATA
1 ATGTATCGATA
213419 TATTCTATCT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTTTAA
Found at i:213452 original size:91 final size:91
Alignment explanation
Indices: 213297--213475 Score: 265
Period size: 91 Copynumber: 2.0 Consensus size: 91
213287 TTTTACCTAG
*
213297 ATGTATCGATACATTTAAAAATGTATCGATACATTCTATTTTTTTACCTAGATGTATCGATACAT
1 ATGTATCGATACATTTAAAAATGTATCGATACATTCTATTTTTTTACCTAGATGTATCAATACAT
*
213362 TTTTCAATGTATCGATACATGTATGA
66 TTTTCAATGTATCGAGACATGTATGA
* * *
213388 ATGTATCGATACATTCT-TAAATGTATTGATATATTCTATCTTTTTT--CTCAGATGTATCAATA
1 ATGTATCGATACATT-TAAAAATGTATCGATACATTCTAT-TTTTTTACCT-AGATGTATCAATA
213450 CATTTTTCAATGTATCGAGACATGTA
63 CATTTTTCAATGTATCGAGACATGTA
213476 GTTAAAATTA
Statistics
Matches: 80, Mismatches: 5, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
90 2 0.03
91 71 0.89
92 7 0.09
ACGTcount: A:0.32, C:0.13, G:0.12, T:0.43
Consensus pattern (91 bp):
ATGTATCGATACATTTAAAAATGTATCGATACATTCTATTTTTTTACCTAGATGTATCAATACAT
TTTTCAATGTATCGAGACATGTATGA
Found at i:225090 original size:97 final size:97
Alignment explanation
Indices: 224843--225079 Score: 359
Period size: 97 Copynumber: 2.4 Consensus size: 97
224833 AAAAATGGGG
* *
224843 TTGGAGTATCCCCTCGGAGGAATGGGGTTGGAGTGTCCCCGATGATGACAATTTTAGTGAGAATA
1 TTGGAGTATCCCCTCGGAGGAATGGGGTTGGAGTGTCCCTGATGATGACAATTTAAGTGAGAATA
*
224908 AAATTTAAACTTTTATGCATTTAAAAGCGGGG
66 AAATTTAAACTTTTATGCATTTAAAAGCGGGA
* **
224940 TTGGAATATCCCCTCGGAGGAATGGGGTTAAAGTGTCCCTGATGATGACAATTTAAGTGAGAATA
1 TTGGAGTATCCCCTCGGAGGAATGGGGTTGGAGTGTCCCTGATGATGACAATTTAAGTGAGAATA
* *
225005 AGATTTAAA-TTTTGATGTATTTAAAAGCGGGA
66 AAATTTAAACTTTT-ATGCATTTAAAAGCGGGA
* * *
225037 TTGGAGTATCCCCTCAGAGGAATAGGGTTGGAGTATCCCTGAT
1 TTGGAGTATCCCCTCGGAGGAATGGGGTTGGAGTGTCCCTGAT
225080 AAATAAAATT
Statistics
Matches: 125, Mismatches: 14, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
96 4 0.03
97 121 0.97
ACGTcount: A:0.30, C:0.13, G:0.27, T:0.30
Consensus pattern (97 bp):
TTGGAGTATCCCCTCGGAGGAATGGGGTTGGAGTGTCCCTGATGATGACAATTTAAGTGAGAATA
AAATTTAAACTTTTATGCATTTAAAAGCGGGA
Found at i:225937 original size:28 final size:28
Alignment explanation
Indices: 225888--226143 Score: 377
Period size: 28 Copynumber: 9.1 Consensus size: 28
225878 GTTTACGGGT
* * *
225888 CCACAAGTTAGTAGCATACTTTCAAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
*
225916 CCATAAGTCAGTGGCATCCTTTCAAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
*
225944 CCACAAGTCAGTGGCATCTTTTCAAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
*
225972 CCACAAGTCAGTGGCATCTTTTCAAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
* * *
226000 CCATAAGTTAGTGGCATCTTTTCAAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
*
226028 CCACAAGTCAGTGGCATCTTTTCAAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
* *
226056 CCATAAGTTAGTGGCATCCTTTCAAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
*
226084 CCACAAGTTAGTGGCATCCTTTCAAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
* *
226112 GCACAAGTCAATGGCATCCTTTCAAAGC
1 CCACAAGTCAGTGGCATCCTTTCAAAGC
226140 CCAC
1 CCAC
226144 GCAAATCGAT
Statistics
Matches: 210, Mismatches: 18, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 210 1.00
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (28 bp):
CCACAAGTCAGTGGCATCCTTTCAAAGC
Found at i:226291 original size:46 final size:46
Alignment explanation
Indices: 226223--226365 Score: 214
Period size: 46 Copynumber: 3.1 Consensus size: 46
226213 ATCAGCAACC
226223 TTTATTAGCTCAATGTCACTGGCCTTGAATCAGCACATTGTCCACT
1 TTTATTAGCTCAATGTCACTGGCCTTGAATCAGCACATTGTCCACT
* *
226269 TTTATTAGCTCAATATCGCTGGCCTTGAATCAGCACATTGTCCACT
1 TTTATTAGCTCAATGTCACTGGCCTTGAATCAGCACATTGTCCACT
** * *
226315 TGTCCCTTAGCTCAATGTCACTAGCCTTGAATCAGCACATTATCCACT
1 T-T-TATTAGCTCAATGTCACTGGCCTTGAATCAGCACATTGTCCACT
226363 TTT
1 TTT
226366 CCCTTAGCTC
Statistics
Matches: 86, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
46 45 0.52
47 2 0.02
48 39 0.45
ACGTcount: A:0.24, C:0.27, G:0.14, T:0.35
Consensus pattern (46 bp):
TTTATTAGCTCAATGTCACTGGCCTTGAATCAGCACATTGTCCACT
Found at i:226344 original size:48 final size:47
Alignment explanation
Indices: 226227--226404 Score: 223
Period size: 48 Copynumber: 3.8 Consensus size: 47
226217 GCAACCTTTA
**
226227 TTAGCTCAATGTCACTGGCCTTGAATCAGCACATTGTCCACTTT-TA
1 TTAGCTCAATGTCACTGGCCTTGAATCAGCACATTGTCCACTTTCCC
* *
226273 TTAGCTCAATATCGCTGGCCTTGAATCAGCACATTGTCCACTTGTCCC
1 TTAGCTCAATGTCACTGGCCTTGAATCAGCACATTGTCCACTT-TCCC
* *
226321 TTAGCTCAATGTCACTAGCCTTGAATCAGCACATTATCCACTTTTCCC
1 TTAGCTCAATGTCACTGGCCTTGAATCAGCACATTGTCCAC-TTTCCC
* ** * **
226369 TTAGCTCGATGTCGTTGGCCTTAAATTGGCACATTG
1 TTAGCTCAATGTCACTGGCCTTGAATCAGCACATTG
226405 GCACTCTTCT
Statistics
Matches: 113, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
46 41 0.36
47 1 0.01
48 69 0.61
49 2 0.02
ACGTcount: A:0.22, C:0.28, G:0.16, T:0.34
Consensus pattern (47 bp):
TTAGCTCAATGTCACTGGCCTTGAATCAGCACATTGTCCACTTTCCC
Found at i:227181 original size:20 final size:20
Alignment explanation
Indices: 227156--227226 Score: 88
Period size: 20 Copynumber: 3.5 Consensus size: 20
227146 TTTTACCCAG
* *
227156 ATGTATCGATATATTTTTCA
1 ATGTATCGATACATTTTTAA
* * *
227176 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTAA
*
227196 ATGTATCGATACATTCTTAA
1 ATGTATCGATACATTTTTAA
227216 ATGTATCGATA
1 ATGTATCGATA
227227 TATTCTATCT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTTTAA
Found at i:228935 original size:11 final size:11
Alignment explanation
Indices: 228911--228949 Score: 71
Period size: 11 Copynumber: 3.6 Consensus size: 11
228901 CCACTAGATG
228911 ATTTTTCAAA-
1 ATTTTTCAAAT
228921 ATTTTTCAAAT
1 ATTTTTCAAAT
228932 ATTTTTCAAAT
1 ATTTTTCAAAT
228943 ATTTTTC
1 ATTTTTC
228950 TTAAAAACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
10 10 0.36
11 18 0.64
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.56
Consensus pattern (11 bp):
ATTTTTCAAAT
Found at i:230127 original size:31 final size:31
Alignment explanation
Indices: 230091--230153 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
230081 AAGTCCCAGA
*
230091 CCCAATTGATGAATTTTTGAAGTACGTAGAC
1 CCCAATTGATGAATTTTTAAAGTACGTAGAC
230122 CCCAATTGATGAATTTTTAAAGTACGTAGAC
1 CCCAATTGATGAATTTTTAAAGTACGTAGAC
230153 C
1 C
230154 ACGGGATCGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Consensus pattern (31 bp):
CCCAATTGATGAATTTTTAAAGTACGTAGAC
Found at i:234135 original size:17 final size:17
Alignment explanation
Indices: 234113--234173 Score: 63
Period size: 17 Copynumber: 3.6 Consensus size: 17
234103 GAATAAATAC
*
234113 AAATATAAAATTAACTT
1 AAATATAAAATTTACTT
* *
234130 AAATATTATATTTA-TT
1 AAATATAAAATTTACTT
*
234146 AAAATATTAAATTTACTT
1 -AAATATAAAATTTACTT
234164 AAA-ATAAAAT
1 AAATATAAAAT
234174 ATTTTTGTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
16 8 0.22
17 27 0.73
18 2 0.05
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (17 bp):
AAATATAAAATTTACTT
Found at i:234177 original size:18 final size:18
Alignment explanation
Indices: 234137--234177 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
234127 CTTAAATATT
*
234137 ATATTTATTAAAATATTA
1 ATATTTATTAAAATATAA
234155 A-ATTTACTTAAAATA-AA
1 ATATTTA-TTAAAATATAA
234172 ATATTT
1 ATATTT
234178 TTGTAAACAC
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (18 bp):
ATATTTATTAAAATATAA
Found at i:238942 original size:22 final size:22
Alignment explanation
Indices: 238914--238955 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
238904 ATAAATAAAA
238914 ATATTTTTAT-ATTAATATTTAT
1 ATATTTTTATAATTAA-ATTTAT
238936 ATATTTTTATAATTAAATTT
1 ATATTTTTATAATTAAATTT
238956 GAATAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
ATATTTTTATAATTAAATTTAT
Found at i:242672 original size:20 final size:20
Alignment explanation
Indices: 242629--242683 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
242619 AGGGTGATTT
*
242629 TGTATCGATACATTTCAGGCA
1 TGTATCGATACA-TTCACGCA
**
242650 TGTATCGATACATTCACTTA
1 TGTATCGATACATTCACGCA
*
242670 TGTTTCGATACATT
1 TGTATCGATACATT
242684 TACTGTTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 18 0.60
21 12 0.40
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.40
Consensus pattern (20 bp):
TGTATCGATACATTCACGCA
Found at i:243389 original size:30 final size:31
Alignment explanation
Indices: 243354--243466 Score: 95
Period size: 31 Copynumber: 3.7 Consensus size: 31
243344 CAGACAAGTG
243354 CCAACTAATGTGGAC-TTGACTCGGGTGCCA
1 CCAACTAATGTGGACTTTGACTCGGGTGCCA
** * *
243384 CCAACTCGTGTGGGCTTTGACTCGGGTGCTGA
1 CCAACTAATGTGGACTTTGACTCGGGTGC-CA
* * * * *
243416 -AAACTTATGTGGGCTTTGACTAGAGTGCCA
1 CCAACTAATGTGGACTTTGACTCGGGTGCCA
* **
243446 CCAATTCGTGTGGACTTTGAC
1 CCAACTAATGTGGACTTTGAC
243467 ATTCTAAGAC
Statistics
Matches: 65, Mismatches: 15, Indels: 5
0.76 0.18 0.06
Matches are distributed among these distances:
30 13 0.20
31 51 0.78
32 1 0.02
ACGTcount: A:0.20, C:0.23, G:0.28, T:0.28
Consensus pattern (31 bp):
CCAACTAATGTGGACTTTGACTCGGGTGCCA
Found at i:243407 original size:31 final size:31
Alignment explanation
Indices: 243369--243466 Score: 108
Period size: 31 Copynumber: 3.2 Consensus size: 31
243359 TAATGTGGAC
243369 TTGACTCGGGTGCCACCAACTCGTGTGGGCT
1 TTGACTCGGGTGCCACCAACTCGTGTGGGCT
* * **
243400 TTGACTCGGGTGCTGA-AAACTTATGTGGGCT
1 TTGACTCGGGTGC-CACCAACTCGTGTGGGCT
* * * *
243431 TTGACTAGAGTGCCACCAATTCGTGTGGACT
1 TTGACTCGGGTGCCACCAACTCGTGTGGGCT
243462 TTGAC
1 TTGAC
243467 ATTCTAAGAC
Statistics
Matches: 53, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
30 1 0.02
31 51 0.96
32 1 0.02
ACGTcount: A:0.18, C:0.22, G:0.30, T:0.30
Consensus pattern (31 bp):
TTGACTCGGGTGCCACCAACTCGTGTGGGCT
Found at i:243555 original size:143 final size:143
Alignment explanation
Indices: 243318--243601 Score: 406
Period size: 143 Copynumber: 2.0 Consensus size: 143
243308 TTTTGTAAGT
* * * * * *
243318 TTTGGCATTCTAAGCCTTGACCTTCTCAGACAAGTGCCAACTAATGTGGACTTGACTCGGGTGCC
1 TTTGACATTCTAAGACTTAACCTCCTCAGACAAGCGCCAACTAATGTGGACTTGACTAGGGTGCC
* * *
243383 ACCAACTCGTGTGGGCTTTGACTCGGGTGCTGAAAACTTATGTGGGCTTTGACTAGAGTGCCACC
66 ACCAACTCGTGTGGGCTTAGACTCGGGTGCCGAAAACTTATGCGGGCTTTGACTAGAGTGCCACC
*
243448 AATTCGTGTGGAC
131 AACTCGTGTGGAC
* *
243461 TTTGACATTCTAAGACTTAACCTCCTTAGACAGGCGCCAACTAATGTGGACTTGACTAGGGTGCC
1 TTTGACATTCTAAGACTTAACCTCCTCAGACAAGCGCCAACTAATGTGGACTTGACTAGGGTGCC
* * ** * *
243526 ACGAACTTGTGTGGGCTTAGACTCGGGTGCCGCTAGCTTGTGCGGGCTTTGACTAGAGTGCCACC
66 ACCAACTCGTGTGGGCTTAGACTCGGGTGCCGAAAACTTATGCGGGCTTTGACTAGAGTGCCACC
243591 AACTCGTGTGG
131 AACTCGTGTGG
243602 GCTTAGACTC
Statistics
Matches: 123, Mismatches: 18, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
143 123 1.00
ACGTcount: A:0.21, C:0.24, G:0.27, T:0.28
Consensus pattern (143 bp):
TTTGACATTCTAAGACTTAACCTCCTCAGACAAGCGCCAACTAATGTGGACTTGACTAGGGTGCC
ACCAACTCGTGTGGGCTTAGACTCGGGTGCCGAAAACTTATGCGGGCTTTGACTAGAGTGCCACC
AACTCGTGTGGAC
Found at i:243609 original size:62 final size:62
Alignment explanation
Indices: 243512--243718 Score: 236
Period size: 62 Copynumber: 3.3 Consensus size: 62
243502 TAATGTGGAC
* *
243512 TTGACTAGGGTGCCACGAACTTGTGTGGGCTTAGACTCGGGTGCCGCTAGCTTGTGCGGGCT
1 TTGACTAGGGTGCCACCAACTTGTGTGGGCTTAGACTCGGGTGCCGCTAGCTTGTACGGGCT
* * * * *
243574 TTGACTAGAGTGCCACCAACTCGTGTGGGCTTAGACTCAGGTGCTGCCAGCTTGTACGGGCT
1 TTGACTAGGGTGCCACCAACTTGTGTGGGCTTAGACTCGGGTGCCGCTAGCTTGTACGGGCT
* * * * ** *
243636 TTAACTCGGGTGCCACCAGCTTATGCAGGCTTTGACTCGGGTGCCG-TCAGCTTGTACGGGCT
1 TTGACTAGGGTGCCACCAACTTGTGTGGGCTTAGACTCGGGTGCCGCT-AGCTTGTACGGGCT
* * * *
243698 TTAATTAGGGTGGCACTAACT
1 TTGACTAGGGTGCCACCAACT
243719 CGTATAAGCT
Statistics
Matches: 120, Mismatches: 24, Indels: 2
0.82 0.16 0.01
Matches are distributed among these distances:
62 120 1.00
ACGTcount: A:0.16, C:0.24, G:0.32, T:0.28
Consensus pattern (62 bp):
TTGACTAGGGTGCCACCAACTTGTGTGGGCTTAGACTCGGGTGCCGCTAGCTTGTACGGGCT
Found at i:243699 original size:31 final size:31
Alignment explanation
Indices: 243512--243699 Score: 169
Period size: 31 Copynumber: 6.1 Consensus size: 31
243502 TAATGTGGAC
* * * * *
243512 TTGACTAGGGTGCCACGAACTTGTGTGGGCT
1 TTGACTCGGGTGCCGCCAGCTTGTGCGGGCT
* *
243543 TAGACTCGGGTGCCGCTAGCTTGTGCGGGCT
1 TTGACTCGGGTGCCGCCAGCTTGTGCGGGCT
* * * * * *
243574 TTGACTAGAGTGCCACCAACTCGTGTGGGCT
1 TTGACTCGGGTGCCGCCAGCTTGTGCGGGCT
* * * *
243605 TAGACTCAGGTGCTGCCAGCTTGTACGGGCT
1 TTGACTCGGGTGCCGCCAGCTTGTGCGGGCT
* * * *
243636 TTAACTCGGGTGCCACCAGCTTATGCAGGCT
1 TTGACTCGGGTGCCGCCAGCTTGTGCGGGCT
* *
243667 TTGACTCGGGTGCCGTCAGCTTGTACGGGCT
1 TTGACTCGGGTGCCGCCAGCTTGTGCGGGCT
243698 TT
1 TT
243700 AATTAGGGTG
Statistics
Matches: 119, Mismatches: 38, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
31 119 1.00
ACGTcount: A:0.15, C:0.25, G:0.32, T:0.28
Consensus pattern (31 bp):
TTGACTCGGGTGCCGCCAGCTTGTGCGGGCT
Found at i:243789 original size:40 final size:40
Alignment explanation
Indices: 243744--243854 Score: 102
Period size: 40 Copynumber: 2.8 Consensus size: 40
243734 AGGAGTGAAC
*
243744 GTCCTGCTCTTTGAGGACAAAAGAAAAAAAGATGAAGT-G
1 GTCCTGCTCTTTGAGGACAAAAGAAAAAAAGATGAAATAG
* * *
243783 AGTCCTGCT-TCTTGAGGATAAAGGGAAAAGAAGGATGAAATAG
1 -GTCCTGCTCT-TTGAGGACAAA-AGAAAA-AAAGATGAAATAG
* * *
243826 GTCCTGCTCCTTAAAGAC-AAAGAAAAAAA
1 GTCCTGCTCTTTGAGGACAAAAGAAAAAAA
243855 AAAGAGAAAA
Statistics
Matches: 56, Mismatches: 10, Indels: 11
0.73 0.13 0.14
Matches are distributed among these distances:
39 3 0.05
40 23 0.41
41 7 0.12
42 22 0.39
43 1 0.02
ACGTcount: A:0.42, C:0.14, G:0.24, T:0.20
Consensus pattern (40 bp):
GTCCTGCTCTTTGAGGACAAAAGAAAAAAAGATGAAATAG
Found at i:245456 original size:17 final size:19
Alignment explanation
Indices: 245417--245458 Score: 52
Period size: 17 Copynumber: 2.3 Consensus size: 19
245407 ATAAAAAATG
245417 TGAAAAGAAAAAAATCGAAT
1 TGAAAAGAAAAAAA-CGAAT
*
245437 TGAAAA-AAAAAAA-GACT
1 TGAAAAGAAAAAAACGAAT
245454 TGAAA
1 TGAAA
245459 TCTTTTCTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 8 0.38
19 7 0.33
20 6 0.29
ACGTcount: A:0.67, C:0.05, G:0.14, T:0.14
Consensus pattern (19 bp):
TGAAAAGAAAAAAACGAAT
Found at i:247994 original size:22 final size:23
Alignment explanation
Indices: 247948--247995 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
247938 CTAAAATATT
* *
247948 TTATTTAAATTAATTAATTACAA
1 TTATTTAAATAAATTAATAACAA
*
247971 TTATTTAAA-AAATTAATAATAA
1 TTATTTAAATAAATTAATAACAA
247993 TTA
1 TTA
247996 AATTGATTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (23 bp):
TTATTTAAATAAATTAATAACAA
Found at i:248007 original size:26 final size:26
Alignment explanation
Indices: 247954--248010 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
247944 TATTTTATTT
247954 AAATTAATTAATTACAATTATTTAAA
1 AAATTAATTAATTACAATTATTTAAA
247980 AAATTAATAATAATTA-AATTGA-TTAAA
1 AAATTAAT--TAATTACAATT-ATTTAAA
248007 AAAT
1 AAAT
248011 AAAAAGAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
26 8 0.29
27 13 0.46
28 7 0.25
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (26 bp):
AAATTAATTAATTACAATTATTTAAA
Found at i:253462 original size:38 final size:38
Alignment explanation
Indices: 253419--253493 Score: 114
Period size: 38 Copynumber: 2.0 Consensus size: 38
253409 TAAGAATTAG
*
253419 GTCAAAATCCCTTAGTCTAAGGGATTCAAATTAGATAA
1 GTCAAAATCCCTTAATCTAAGGGATTCAAATTAGATAA
* * *
253457 GTCAAAATCTCTTAATTTAAGGGATTTAAATTAGATA
1 GTCAAAATCCCTTAATCTAAGGGATTCAAATTAGATA
253494 GTTACCATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (38 bp):
GTCAAAATCCCTTAATCTAAGGGATTCAAATTAGATAA
Found at i:253698 original size:30 final size:30
Alignment explanation
Indices: 253664--253724 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
253654 TTTGAAACTG
* *
253664 GGAA-TTTTTTTCTATTCAGCCTTCATTACT
1 GGAATTTTTTTTCTAAT-AGCCTTAATTACT
253694 GGAATTTTTTTTCTAATAGCCTTAATTACT
1 GGAATTTTTTTTCTAATAGCCTTAATTACT
253724 G
1 G
253725 CTGTTCAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 17 0.61
31 11 0.39
ACGTcount: A:0.23, C:0.16, G:0.11, T:0.49
Consensus pattern (30 bp):
GGAATTTTTTTTCTAATAGCCTTAATTACT
Found at i:256312 original size:30 final size:30
Alignment explanation
Indices: 256276--256337 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
256266 TCGATTCACT
*
256276 CACTGAACCCATAACATCTCCCGTCCCAGC
1 CACTGAACCCATAACATCTCCCATCCCAGC
* * *
256306 CACTGAACCTATGACATCTCCTATCCCAGC
1 CACTGAACCCATAACATCTCCCATCCCAGC
256336 CA
1 CA
256338 ATGTCATTCC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.27, C:0.44, G:0.10, T:0.19
Consensus pattern (30 bp):
CACTGAACCCATAACATCTCCCATCCCAGC
Found at i:260262 original size:15 final size:16
Alignment explanation
Indices: 260242--260272 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
260232 ATTTGAACAC
260242 AAAAATAA-TAAAATA
1 AAAAATAATTAAAATA
260257 AAAAATAATTAAAATA
1 AAAAATAATTAAAATA
260273 TAACATAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (16 bp):
AAAAATAATTAAAATA
Found at i:260627 original size:1 final size:1
Alignment explanation
Indices: 260621--260645 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
260611 CCTCCAAACA
260621 CCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCC
260646 AAAAAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:265286 original size:155 final size:155
Alignment explanation
Indices: 265004--265312 Score: 476
Period size: 155 Copynumber: 2.0 Consensus size: 155
264994 CTGAAATATG
* *
265004 AAAATGCCCTATTTAGAATGTGTCACCTCAATTCCTAGGAAGTACTTCAATCTTCCCAACTACTT
1 AAAATGCCCTATTTAGAATGTGCCACCTCAATTCCTAGGAAGCACTTCAATCTTCCCAACTACTT
* * *
265069 AATCCTAAATTCTTTGTTTAGACACTACCTTAGGGACTCCTTTTCAAATTTATCATTCCCAATCA
66 AATCCTAAATTCTTTGATCAGACACTACCTTAGGGACTCCTTTTCAAATTCATCATTCCCAATCA
265134 TTATTATATCATCAACATATACTAA
131 TTATTATATCATCAACATATACTAA
* * * * **
265159 AAAATGCCCTGTTTAGAATGTGCCATCTTAATTCTTAGGAAGCACTTCAATCTTCCCAACTGTTT
1 AAAATGCCCTATTTAGAATGTGCCACCTCAATTCCTAGGAAGCACTTCAATCTTCCCAACTACTT
* * *
265224 AAT-CTCAAATTCTTTGATCAGACACTACCTTATGGACTCCTTTTCAGATTCATCATTCCCAATT
66 AATCCT-AAATTCTTTGATCAGACACTACCTTAGGGACTCCTTTTCAAATTCATCATTCCCAATC
265288 ATTATTATATCATCAACATATACTA
130 ATTATTATATCATCAACATATACTA
265313 GCAAAACTAT
Statistics
Matches: 139, Mismatches: 14, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
154 2 0.01
155 137 0.99
ACGTcount: A:0.31, C:0.24, G:0.08, T:0.37
Consensus pattern (155 bp):
AAAATGCCCTATTTAGAATGTGCCACCTCAATTCCTAGGAAGCACTTCAATCTTCCCAACTACTT
AATCCTAAATTCTTTGATCAGACACTACCTTAGGGACTCCTTTTCAAATTCATCATTCCCAATCA
TTATTATATCATCAACATATACTAA
Found at i:271416 original size:15 final size:14
Alignment explanation
Indices: 271383--271434 Score: 54
Period size: 15 Copynumber: 3.6 Consensus size: 14
271373 GTATACTTTG
*
271383 TTAATTTTATTAATT
1 TTAATTTTATTAA-A
271398 TTAATTTTAATTAAA
1 TTAATTTT-ATTAAA
271413 TTAA-TTTA-TATAA
1 TTAATTTTATTA-AA
271426 TTAATTTTA
1 TTAATTTTA
271435 AAAAATAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
12 2 0.06
13 7 0.21
14 7 0.21
15 12 0.36
16 5 0.15
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
TTAATTTTATTAAA
Found at i:271457 original size:28 final size:29
Alignment explanation
Indices: 271384--271457 Score: 75
Period size: 28 Copynumber: 2.6 Consensus size: 29
271374 TATACTTTGT
* *
271384 TAAT-TTTATTAATTTTAATTTTAATTAAA
1 TAATATTTAATAA-TTTAATTTTAATAAAA
*
271413 TTA-ATTTATATAA-TTAATTTTAA-AAAA
1 TAATATTTA-ATAATTTAATTTTAATAAAA
271440 TAATATTTAATAATTTAA
1 TAATATTTAATAATTTAA
271458 GATTTAAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
27 9 0.24
28 19 0.51
29 6 0.16
30 3 0.08
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (29 bp):
TAATATTTAATAATTTAATTTTAATAAAA
Found at i:284819 original size:62 final size:63
Alignment explanation
Indices: 284749--284867 Score: 213
Period size: 63 Copynumber: 1.9 Consensus size: 63
284739 AGTTCAATAT
* *
284749 CTAGGAAAGGAAAAATGATTT-AAAAAAGAAAGTTATAAAGTACATTTTAACGTTTTCAAGTG
1 CTAGGAAAGGAAAAATGATTTAAAAAAAGAAAGATATAAAGTACATTTTAAAGTTTTCAAGTG
284811 CTAGGAAAGGAAAAATGATTTAAAAAAAGAAAGATATAAAGTACATTTTAAAGTTTT
1 CTAGGAAAGGAAAAATGATTTAAAAAAAGAAAGATATAAAGTACATTTTAAAGTTTT
284868 TGTCATTGAT
Statistics
Matches: 54, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
62 21 0.39
63 33 0.61
ACGTcount: A:0.50, C:0.05, G:0.17, T:0.29
Consensus pattern (63 bp):
CTAGGAAAGGAAAAATGATTTAAAAAAAGAAAGATATAAAGTACATTTTAAAGTTTTCAAGTG
Found at i:286435 original size:2 final size:2
Alignment explanation
Indices: 286428--286455 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
286418 TACACATTAA
286428 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
286456 GAGGGATTAA
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:293148 original size:14 final size:15
Alignment explanation
Indices: 293129--293162 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
293119 TACTAATGGT
293129 TTTTTG-GATTTTTA
1 TTTTTGTGATTTTTA
*
293143 TTTTTGTGTTTTTTA
1 TTTTTGTGATTTTTA
293158 TTTTT
1 TTTTT
293163 TCATTTGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.09, C:0.00, G:0.12, T:0.79
Consensus pattern (15 bp):
TTTTTGTGATTTTTA
Found at i:295088 original size:2 final size:2
Alignment explanation
Indices: 295081--295124 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
295071 CCATCAATAC
295081 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
295123 AT
1 AT
295125 GAAAATTTAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:295328 original size:32 final size:32
Alignment explanation
Indices: 295292--295361 Score: 104
Period size: 32 Copynumber: 2.2 Consensus size: 32
295282 AGATTCACTT
* * *
295292 ATTAATTGTAACAATCATATTTATGAATAACG
1 ATTAATTGTAAAAATCATACTTATAAATAACG
*
295324 ATTAATTGTAAAAATCATACTTATAAATAATG
1 ATTAATTGTAAAAATCATACTTATAAATAACG
295356 ATTAAT
1 ATTAAT
295362 CATATATTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.39
Consensus pattern (32 bp):
ATTAATTGTAAAAATCATACTTATAAATAACG
Found at i:295389 original size:15 final size:15
Alignment explanation
Indices: 295369--295397 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
295359 AATCATATAT
295369 TAAAAAATAATAAAC
1 TAAAAAATAATAAAC
295384 TAAAAAATAATAAA
1 TAAAAAATAATAAA
295398 AAGAAACCAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (15 bp):
TAAAAAATAATAAAC
Found at i:307214 original size:78 final size:79
Alignment explanation
Indices: 306941--307252 Score: 314
Period size: 79 Copynumber: 4.0 Consensus size: 79
306931 TATTTTGGAG
* * * * * * *
306941 AAAAA-AACGAGGTTGGAG-AATCCCTGA-TGATGAAAAGTCGATATTTTGGAAACAAAATTGGG
1 AAAAATAACGGGGTTGGAGTATTCCC-GATTG-TGAAAAATCGATGTTTTAGAAATAAAACTGGG
*
307003 GTTGGAGTATCCTCTT
64 GTTTGAGTATCCTCTT
* * * * *
307019 GAAAATAACGGGGTTGGAGTA-TCTCTGATGGTAAAAAATCGGTGTTTTAGAAATAAAACTGGGG
1 AAAAATAACGGGGTTGGAGTATTC-CCGATTGTGAAAAATCGATGTTTTAGAAATAAAACTGGGG
*
307083 -TTGACGTATCCTCTC
65 TTTGA-GTATCCTCTT
* * * * *
307098 AGAAATAACGGGGTTGGAGTATTCTCGATTTTGAAAAATCGATGTTTAAGAAAT-AAAGTCGGGG
1 AAAAATAACGGGGTTGGAGTATTCCCGATTGTGAAAAATCGATGTTTTAGAAATAAAACT-GGGG
307162 TTTGAGTATCC-CTT
65 TTTGAGTATCCTCTT
* * * *
307176 AAAAATAATGGGGTTGGAGTATTCCCGATTGTGAAAAATTGATGTTTTGGAAATAAAACTAGGGT
1 AAAAATAACGGGGTTGGAGTATTCCCGATTGTGAAAAATCGATGTTTTAGAAATAAAACTGGGGT
*
307241 TGGAGTATCCTC
66 TTGAGTATCCTC
307253 GATGGTGGAA
Statistics
Matches: 190, Mismatches: 34, Indels: 19
0.78 0.14 0.08
Matches are distributed among these distances:
78 73 0.38
79 108 0.57
80 9 0.05
ACGTcount: A:0.33, C:0.11, G:0.26, T:0.30
Consensus pattern (79 bp):
AAAAATAACGGGGTTGGAGTATTCCCGATTGTGAAAAATCGATGTTTTAGAAATAAAACTGGGGT
TTGAGTATCCTCTT
Found at i:309797 original size:50 final size:51
Alignment explanation
Indices: 309702--309836 Score: 202
Period size: 50 Copynumber: 2.7 Consensus size: 51
309692 AAAAATGCTT
* * *
309702 GAATGTATCGATACATTG-AGAATGTATCGATATATCTAGGTTAAAACCCA
1 GAATGTATCGATACAATGAAGAATGTATCGATACATCTAGGGTAAAACCCA
* *
309752 GAATGTATCGATACAATGAAAAATGTATCGATACAT-TTGGGTAAAACCCA
1 GAATGTATCGATACAATGAAGAATGTATCGATACATCTAGGGTAAAACCCA
*
309802 GAATGTATCGATACAATGAAGGATGTATCGATACA
1 GAATGTATCGATACAATGAAGAATGTATCGATACA
309837 AATTGTGAAA
Statistics
Matches: 77, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
50 62 0.81
51 15 0.19
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.27
Consensus pattern (51 bp):
GAATGTATCGATACAATGAAGAATGTATCGATACATCTAGGGTAAAACCCA
Found at i:311656 original size:14 final size:15
Alignment explanation
Indices: 311639--311668 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
311629 TGATTATTAA
311639 TTTTAATTT-TTTAT
1 TTTTAATTTATTTAT
311653 TTTTAATTTATTTAT
1 TTTTAATTTATTTAT
311668 T
1 T
311669 ATTTTAATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTAATTTATTTAT
Found at i:313407 original size:2 final size:2
Alignment explanation
Indices: 313400--313428 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
313390 ATTTTTCTTG
313400 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
313429 AAGATATAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:313900 original size:2 final size:2
Alignment explanation
Indices: 313857--313888 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
313847 ATGTGTTTAT
*
313857 TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
313889 CAACTTTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:314783 original size:21 final size:22
Alignment explanation
Indices: 314746--314787 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
314736 AAATAAATGC
314746 AATTAATAAGCATATATTATAG
1 AATTAATAAGCATATATTATAG
*
314768 AATTAATAA-TATATATTATA
1 AATTAATAAGCATATATTATA
314788 ATAAAATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.40
Consensus pattern (22 bp):
AATTAATAAGCATATATTATAG
Found at i:315393 original size:2 final size:2
Alignment explanation
Indices: 315386--315415 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
315376 ATTTTGAAAT
315386 TA TA TA TA TA TA TA TA TA TA TA TA TCA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T
315416 TAGGCACTGG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:316072 original size:81 final size:78
Alignment explanation
Indices: 315912--316099 Score: 331
Period size: 81 Copynumber: 2.4 Consensus size: 78
315902 GAGTATCTCC
315912 GAGAATGTAAATTTAAGATTTTTTTGTAAAATGAGATTGGAGTATCCACTTTTGAAGAGATACGG
1 GAGAATGTAAATTTAAGATTTTTTTGTAAAATGAGATTGGAGTATCCACTTTTGAAGAGATACGG
315977 TTGGAAAATCCCT
66 TTGGAAAATCCCT
*
315990 GAGAATGTAAATTTAAGATTTTTTTGTAAAATGTGATTGGAATAGTATCCACTTTTGAAGAGATA
1 GAGAATGTAAATTTAAGATTTTTTTGTAAAATGAGATTGG---AGTATCCACTTTTGAAGAGATA
316055 CGGTTGGAAAATCCCT
63 CGGTTGGAAAATCCCT
*
316071 GAGAATGTAAATTAAAGATTTTTTTGTAA
1 GAGAATGTAAATTTAAGATTTTTTTGTAA
316100 GAGAAATAGG
Statistics
Matches: 105, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
78 39 0.37
81 66 0.63
ACGTcount: A:0.36, C:0.07, G:0.21, T:0.36
Consensus pattern (78 bp):
GAGAATGTAAATTTAAGATTTTTTTGTAAAATGAGATTGGAGTATCCACTTTTGAAGAGATACGG
TTGGAAAATCCCT
Found at i:316168 original size:79 final size:77
Alignment explanation
Indices: 316070--316374 Score: 326
Period size: 79 Copynumber: 3.9 Consensus size: 77
316060 GGAAAATCCC
* * *
316070 TGAGAATGTAAATTAAAGATTTTTTTGTAAGAGAAATAGGGTTGGAGTATCCCTCAGAGAGATAA
1 TGAGAATGTAAATTCAAGA-TTTTTTGTAAGAAAAATAGGGTTAGAGTATCCCTCAGAGAGATAA
* *
316135 AGTTGGCATTACCT
65 AGTTAG-AGTACCT
* * ** *
316149 TGAAAATGCAAATTCAAGATTTTTTGTAAGAAAAAT-GGAGTTAGAGTATCCCTTTGGAGAGTTA
1 TGAGAATGTAAATTCAAGATTTTTTGTAAGAAAAATAGG-GTTAGAGTATCCC-TCAGAGAGATA
* *
316213 GAGTCAGAGTACCCT
64 AAGTTAGAGTA-CCT
* * * * * *
316228 TGAGAATGTAAATTTAAGTTTTTTTTATAAGAAAAATTGAGTTAGAGTATTCTCTCAGAGAGATA
1 TGAGAATGTAAATTCAAG-ATTTTTTGTAAGAAAAATAGGGTTAGAGTA-TCCCTCAGAGAGATA
316293 AAGTTAGAGTACCT
64 AAGTTAGAGTACCT
* * * *
316307 TCGAGAATGTAAATTCAAGATTTTTTGTAAGAAAAA-AAGGTTAGAGTATCCATCGGAGAGATAG
1 T-GAGAATGTAAATTCAAGATTTTTTGTAAGAAAAATAGGGTTAGAGTATCCCTCAGAGAGATAA
316371 AGTT
65 AGTT
316375 GGACATCCTT
Statistics
Matches: 185, Mismatches: 34, Indels: 16
0.79 0.14 0.07
Matches are distributed among these distances:
77 18 0.10
78 40 0.22
79 65 0.35
80 58 0.31
81 4 0.02
ACGTcount: A:0.37, C:0.09, G:0.22, T:0.32
Consensus pattern (77 bp):
TGAGAATGTAAATTCAAGATTTTTTGTAAGAAAAATAGGGTTAGAGTATCCCTCAGAGAGATAAA
GTTAGAGTACCT
Found at i:316172 original size:159 final size:155
Alignment explanation
Indices: 315993--316336 Score: 347
Period size: 158 Copynumber: 2.2 Consensus size: 155
315983 AATCCCTGAG
* *
315993 AATGTAAATTTAAGATTTTTTTGTAAAATGTGA-TTGGAATAGTATCCACTTTTGAAGAGATACG
1 AATGTAAATTCAAGA-TTTTTTGTAAAATG-GAGTT---AGAGTATCC-C-TTTGAAGAGATA-G
** * * * *
316057 -GTTGGAAAATCCC-TGAGAATGTAAATTAAAGATTTTTTTGTAAGAGAAATAGGGTTGGAGTA-
58 AGTCAGAAAA-CCCTTGAGAATGTAAATTAAAGATTTTTTTATAAGAAAAATAGAGTTAGAGTAT
* *
316119 TCCCTCAGAGAGATAAAGTTGGCATTACCTT-GAA
122 TCCCTCAGAGAGATAAAGTTAG-AGTACCTTCGAA
* * *
316153 AATGCAAATTCAAGATTTTTTGTAAGAAAAATGGAGTTAGAGTATCCCTTTGGAGAGTTAGAGTC
1 AATGTAAATTCAAGATTTTTTGT----AAAATGGAGTTAGAGTATCCCTTTGAAGAGATAGAGTC
** * * * *
316218 AGAGTACCCTTGAGAATGTAAATTTAAGTTTTTTTTATAAGAAAAATTGAGTTAGAGTATTCTCT
62 AGAAAACCCTTGAGAATGTAAATTAAAGATTTTTTTATAAGAAAAATAGAGTTAGAGTATTCCCT
*
316283 CAGAGAGATAAAGTTAGAGTACCTTCGAG
127 CAGAGAGATAAAGTTAGAGTACCTTCGAA
316312 AATGTAAATTCAAGATTTTTTGTAA
1 AATGTAAATTCAAGATTTTTTGTAA
316337 GAAAAAAAGG
Statistics
Matches: 154, Mismatches: 21, Indels: 23
0.78 0.11 0.12
Matches are distributed among these distances:
155 2 0.01
157 4 0.03
158 64 0.42
159 53 0.34
160 21 0.14
162 2 0.01
163 8 0.05
ACGTcount: A:0.36, C:0.09, G:0.21, T:0.34
Consensus pattern (155 bp):
AATGTAAATTCAAGATTTTTTGTAAAATGGAGTTAGAGTATCCCTTTGAAGAGATAGAGTCAGAA
AACCCTTGAGAATGTAAATTAAAGATTTTTTTATAAGAAAAATAGAGTTAGAGTATTCCCTCAGA
GAGATAAAGTTAGAGTACCTTCGAA
Found at i:316251 original size:158 final size:158
Alignment explanation
Indices: 316070--316357 Score: 418
Period size: 158 Copynumber: 1.8 Consensus size: 158
316060 GGAAAATCCC
* * * *
316070 TGAGAATGTAAATTAAAGATTTTTTTGTAAGAGAAATAGGGTTGGAGTA-TCCCTCAGAGAGATA
1 TGAGAATGTAAATTAAAGATTTTTTTATAAGAAAAATAGAGTTAGAGTATTCCCTCAGAGAGATA
* * **
316134 AAGTTGGCATTACCTT-GAAAATGCAAATTCAAGATTTTTTGTAAGAAAAATGGAGTTAGAGTAT
66 AAGTTAG-AGTACCTTCGAAAATGCAAATTCAAGATTTTTTGTAAGAAAAAAAG-GTTAGAGTAT
316198 CCCTTTGGAGAGTTAGAGTCAGAGTACCCT
129 CCCTTTGGAGAGTTAGAGTCAGAGTACCCT
* * * *
316228 TGAGAATGTAAATTTAAGTTTTTTTTATAAGAAAAATTGAGTTAGAGTATTCTCTCAGAGAGATA
1 TGAGAATGTAAATTAAAGATTTTTTTATAAGAAAAATAGAGTTAGAGTATTCCCTCAGAGAGATA
* *
316293 AAGTTAGAGTACCTTCGAGAATGTAAATTCAAGATTTTTTGTAAGAAAAAAAGGTTAGAGTATCC
66 AAGTTAGAGTACCTTCGAAAATGCAAATTCAAGATTTTTTGTAAGAAAAAAAGGTTAGAGTATCC
316358 ATCGGAGAGA
Statistics
Matches: 114, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
158 61 0.54
159 53 0.46
ACGTcount: A:0.37, C:0.09, G:0.22, T:0.33
Consensus pattern (158 bp):
TGAGAATGTAAATTAAAGATTTTTTTATAAGAAAAATAGAGTTAGAGTATTCCCTCAGAGAGATA
AAGTTAGAGTACCTTCGAAAATGCAAATTCAAGATTTTTTGTAAGAAAAAAAGGTTAGAGTATCC
CTTTGGAGAGTTAGAGTCAGAGTACCCT
Found at i:318767 original size:75 final size:74
Alignment explanation
Indices: 318643--318784 Score: 203
Period size: 75 Copynumber: 1.9 Consensus size: 74
318633 GAGTGTGTTC
*
318643 AACTAATGTCAAGTATTAAGGGACAACTCCAGGTATTATGCTCAACTACTCTCATTTCTATTAGT
1 AACTAATGTCAAGTATTAAGGGACAACTCCAGGTACTATGCTCAACTACTCTCATTTCTATT-GT
318708 TCTGTCGTGT
65 TCTGTCGTGT
* * * * * * *
318718 AACTAATGTCGAGTATTAGGGGACAACTCTAGGTACTATGCTTAGCTACTTTCATTTTTATTGTT
1 AACTAATGTCAAGTATTAAGGGACAACTCCAGGTACTATGCTCAACTACTCTCATTTCTATTGTT
318783 CT
66 CT
318785 ACTGTGCAGA
Statistics
Matches: 59, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
74 5 0.08
75 54 0.92
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.38
Consensus pattern (74 bp):
AACTAATGTCAAGTATTAAGGGACAACTCCAGGTACTATGCTCAACTACTCTCATTTCTATTGTT
CTGTCGTGT
Found at i:319300 original size:23 final size:23
Alignment explanation
Indices: 319224--319300 Score: 57
Period size: 23 Copynumber: 3.3 Consensus size: 23
319214 AATTTCAATC
*
319224 AAAAAATAAACACATAAATAAAT
1 AAAAAATAAACACATAAATAATT
* * * **
319247 ACATAAAT-CACATATATTTAATT
1 A-AAAAATAAACACATAAATAATT
* * *
319270 ACACAATAAACACATAAGTAATT
1 AAAAAATAAACACATAAATAATT
319293 AAAAAATA
1 AAAAAATA
319301 TATGAAAATT
Statistics
Matches: 37, Mismatches: 15, Indels: 4
0.66 0.27 0.07
Matches are distributed among these distances:
22 3 0.08
23 29 0.78
24 5 0.14
ACGTcount: A:0.62, C:0.12, G:0.01, T:0.25
Consensus pattern (23 bp):
AAAAAATAAACACATAAATAATT
Found at i:319695 original size:18 final size:18
Alignment explanation
Indices: 319672--319707 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
319662 TTTTTTAGTT
319672 TTTTATAATTATTTTATA
1 TTTTATAATTATTTTATA
* *
319690 TTTTATAGTTTTTTTATA
1 TTTTATAATTATTTTATA
319708 AATTTTTTAA
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:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (18 bp):
TTTTATAATTATTTTATA
Found at i:319702 original size:29 final size:28
Alignment explanation
Indices: 319662--319716 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 28
319652 TTGTTTCAAT
*
319662 TTTTTTAGTTTTTTAT-AATTATTTTATA
1 TTTTATAGTTTTTTATAAATT-TTTTATA
319690 TTTTATAGTTTTTTTATAAATTTTTTA
1 TTTTATAG-TTTTTTATAAATTTTTTA
319717 AACATTTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 7 0.29
29 13 0.54
30 4 0.17
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.71
Consensus pattern (28 bp):
TTTTATAGTTTTTTATAAATTTTTTATA
Found at i:319770 original size:15 final size:16
Alignment explanation
Indices: 319750--319788 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
319740 TATATTATTA
**
319750 ATTTTTTTG-GACTTT
1 ATTTTTTTGAGAAGTT
319765 ATTTTTTTGAGAAGTT
1 ATTTTTTTGAGAAGTT
319781 ATTTTTTT
1 ATTTTTTT
319789 TTGTTTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 9 0.43
16 12 0.57
ACGTcount: A:0.18, C:0.03, G:0.13, T:0.67
Consensus pattern (16 bp):
ATTTTTTTGAGAAGTT
Found at i:319886 original size:20 final size:20
Alignment explanation
Indices: 319839--319887 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
319829 AGATCTTGTA
* *
319839 ATTTTTTTGGGTTTTGCTTT
1 ATTTTTTTGAGTTTTGCATT
*
319859 ACTATTTTT-AGTTTTGCATT
1 A-TTTTTTTGAGTTTTGCATT
319879 ATTTTTTTG
1 ATTTTTTTG
319888 TTAAGTCTCT
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
19 6 0.26
20 11 0.48
21 6 0.26
ACGTcount: A:0.12, C:0.06, G:0.14, T:0.67
Consensus pattern (20 bp):
ATTTTTTTGAGTTTTGCATT
Found at i:323201 original size:290 final size:290
Alignment explanation
Indices: 322676--323263 Score: 1158
Period size: 290 Copynumber: 2.0 Consensus size: 290
322666 AGGCCCGCCA
*
322676 TCATCGTTCACATCCTTTAGCTTAGCATATAACTTAATTATGTCAACATTAAGGAATTGTTTATG
1 TCATTGTTCACATCCTTTAGCTTAGCATATAACTTAATTATGTCAACATTAAGGAATTGTTTATG
322741 GGCATCACACATGCATTTCACATCATCATCATCTTCAACTGAGAAACTCCTATATCGGACATATC
66 GGCATCACACATGCATTTCACATCATCATCATCTTCAACTGAGAAACTCCTATATCGGACATATC
322806 TTCCCTCATAGAAATAAAAAGCCTATACTTGATCTCTGATACTCTTCTTCTGTTCCCAGCTTTGA
131 TTCCCTCATAGAAATAAAAAGCCTATACTTGATCTCTGATACTCTTCTTCTGTTCCCAGCTTTGA
322871 TTTTTGTATTAATGATGGCCTTTAATTCCTCTATTATGATGTCTTCCTCAAAACTAATACTTTTT
196 TTTTTGTATTAATGATGGCCTTTAATTCCTCTATTATGATGTCTTCCTCAAAACTAATACTTTTT
322936 AGACGATCACTTTGGAAAGTAACACCTTAT
261 AGACGATCACTTTGGAAAGTAACACCTTAT
322966 TCATTGTTCACATCCTTTAGCTTAGCATATAACTTAATTATGTCAACATTAAGGAATTGTTTATG
1 TCATTGTTCACATCCTTTAGCTTAGCATATAACTTAATTATGTCAACATTAAGGAATTGTTTATG
323031 GGCATCACACATGCATTTCACATCATCATCATCTTCAACTGAGAAACTCCTATATCGGACATATC
66 GGCATCACACATGCATTTCACATCATCATCATCTTCAACTGAGAAACTCCTATATCGGACATATC
323096 TTCCCTCATAGAAATAAAAAGCCTATACTTGATCTCTGATACTCTTCTTCTGTTCCCAGCTTTGA
131 TTCCCTCATAGAAATAAAAAGCCTATACTTGATCTCTGATACTCTTCTTCTGTTCCCAGCTTTGA
*
323161 TTTTTGTATTAATTATGGCCTTTAATTCCTCTATTATGATGTCTTCCTCAAAACTAATACTTTTT
196 TTTTTGTATTAATGATGGCCTTTAATTCCTCTATTATGATGTCTTCCTCAAAACTAATACTTTTT
323226 AGACGATCACTTTGGAAAGTAACACCTTAT
261 AGACGATCACTTTGGAAAGTAACACCTTAT
323256 TCATTGTT
1 TCATTGTT
323264 GAAAATTTGT
Statistics
Matches: 296, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
290 296 1.00
ACGTcount: A:0.29, C:0.22, G:0.11, T:0.38
Consensus pattern (290 bp):
TCATTGTTCACATCCTTTAGCTTAGCATATAACTTAATTATGTCAACATTAAGGAATTGTTTATG
GGCATCACACATGCATTTCACATCATCATCATCTTCAACTGAGAAACTCCTATATCGGACATATC
TTCCCTCATAGAAATAAAAAGCCTATACTTGATCTCTGATACTCTTCTTCTGTTCCCAGCTTTGA
TTTTTGTATTAATGATGGCCTTTAATTCCTCTATTATGATGTCTTCCTCAAAACTAATACTTTTT
AGACGATCACTTTGGAAAGTAACACCTTAT
Found at i:323727 original size:75 final size:75
Alignment explanation
Indices: 323589--323735 Score: 206
Period size: 75 Copynumber: 2.0 Consensus size: 75
323579 CCACATGCGT
* * *
323589 TTGTCACATCTTTCAGGTTCTAAGAAATTTATTAGGTATTAGTCAAATATTTTTCGTCATGTCAG
1 TTGTCACATCTTTCAGGTTCCAAGAAATTTATTAGGTATCAGTCAAATATTTTTCATCATGTCAG
323654 AAGGAATCTG
66 AAGGAATCTG
* ** *
323664 TTGTCACATTTTTTGGGTTCCAAGAAATTTATTAGGTATCAGTCAAATA-TTTTCTATCGTGTCA
1 TTGTCACATCTTTCAGGTTCCAAGAAATTTATTAGGTATCAGTCAAATATTTTTC-ATCATGTCA
*
323728 GACGGAAT
65 GAAGGAAT
323736 TTGATACCCA
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
74 5 0.08
75 58 0.92
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.40
Consensus pattern (75 bp):
TTGTCACATCTTTCAGGTTCCAAGAAATTTATTAGGTATCAGTCAAATATTTTTCATCATGTCAG
AAGGAATCTG
Found at i:324315 original size:535 final size:536
Alignment explanation
Indices: 323298--324587 Score: 2228
Period size: 535 Copynumber: 2.4 Consensus size: 536
323288 AAGTGCGACA
323298 AATCTATTACTCATCTTGTTTAAGTACGAGAAATAAATACCTACAATTGGGTTTATAGTAGGCAA
1 AATCTATTACTCATCTTGTTTAAGTACGAGAAATAAATACCTACAATTGGGTTTATAGTAGGCAA
*
323363 GAAAGGCTAGAATAAAGAAGCACTATCAATAAATTTTACAAACAAATCTTGCATAAATTGGAAAG
66 GAAAGGCTAGAATAAAGAAGCACTATCAATAAACTTTACAAACAAATCTTGCATAAATTGGAAAG
*
323428 AAAATGACAATGAAAGTGATTGAAAATGAGAATAATGAACTAAGTATTTATAATGGAGTAAAAAA
131 AAAATGACAATGAAAGTGAATGAAAATGAGAATAAT--ACTAAGTATTTATAATGGAGTAAAAAA
*
323493 TATCTATGCACCAATTTCAC--TTTTTTTTTACATTCTGTCTTATCATTAGTCAAATATTTTCTA
194 TATCTATGCACCAATTTCACTTTTTTTTTTTACATTCTGTCATATCATTAGTCAAATATTTTCTA
* * * *
323556 TCGTATTAGAAAGAATCTAATACCCACATGCGTTTGTCACATCTTTCAGGTTCTAAGAAATTTAT
259 GCGTATCAGAAAGAATCTAATACCCACATGCGTTTATCACATCTTTCAGGTTCTAAAAAATTTAT
* **
323621 TAGGTATTAGTCAAATATTTTTCGTCATGTCAGAAGGAATCTGTTGTCACATTTTTTGGGTTCCA
324 TAGGTATTAGTCAAATATTTTTCGTCATGTCAAAAGGAATCTGTTGTCACATTTTTCAGGTTCCA
* *
323686 AGAAATTTATTAGGTATCAGTCAAATATTTTCTATCGTGTCAGACGGAATTTGATACCCACATGT
389 AGAAATTTATTAGGTATCAGTCAAATATTATCTATCGTGTCAGAAGGAATTTGATACCCACATGT
* * * *
323751 GTAGACACCTCATTTTGTCCGGGCCAATTTTTGACAACTTGAGGCTTATCTAGTAGGTGGAGGAT
454 GTAGACACCTCATTTTGTCCAGACCAATTTTTGACAACTTGAGGCCTAGCTAGTAGGTGGAGGAT
323816 TGGACATGTGTGGGGACG
519 TGGACATGTGTGGGGACG
* *
323834 AATCTATTACTCATTTTGTTTAAGTACGAGAAATAAATACCTACAATTGGGTTTATAATAGGCAA
1 AATCTATTACTCATCTTGTTTAAGTACGAGAAATAAATACCTACAATTGGGTTTATAGTAGGCAA
*
323899 GAAAGGCTAGAATAAAGAAGCACTATCAATAAACTTTACAAACAAATCTTGCATAAATTGGAAAT
66 GAAAGGCTAGAATAAAGAAGCACTATCAATAAACTTTACAAACAAATCTTGCATAAATTGGAAAG
*
323964 AAAATGACAATGAAAATGAATGAAAATGAGAATAAT-CTAAGTATTTATAATGGAGTAAAAAATA
131 AAAATGACAATGAAAGTGAATGAAAATGAGAATAATACTAAGTATTTATAATGGAGTAAAAAATA
*
324028 TCTATGCACCAATTTCACTTTTTTTTTTTACATTCTGTCATATCATTAGTCAAATATTTTCTGGC
196 TCTATGCACCAATTTCACTTTTTTTTTTTACATTCTGTCATATCATTAGTCAAATATTTTCTAGC
* * *
324093 GTGTCAGAAAGAATCTGATACCCACATGCGTTTATCACATCTTTCGGGTTCTAAAAAATTTATTA
261 GTATCAGAAAGAATCTAATACCCACATGCGTTTATCACATCTTTCAGGTTCTAAAAAATTTATTA
324158 GGTATTAGTCAAATATTTTTCGTCATGTCAAAAGGAATCTGTTGTCACATTTTTCAGGTTCCAAG
326 GGTATTAGTCAAATATTTTTCGTCATGTCAAAAGGAATCTGTTGTCACATTTTTCAGGTTCCAAG
*
324223 AAATTTATTAGGTATTAGTCAAATATTATCTATCGTG-CTAGAAGGAATTTGATACCCACATGTG
391 AAATTTATTAGGTATCAGTCAAATATTATCTATCGTGTC-AGAAGGAATTTGATACCCACATGTG
324287 TAGACACCTCATTTTGTCCAGACCAATTTTTGACAACTTGAGGCCTAGCTAGTAGGTGGAGGATT
455 TAGACACCTCATTTTGTCCAGACCAATTTTTGACAACTTGAGGCCTAGCTAGTAGGTGGAGGATT
324352 GGACATGTGTGGGGACG
520 GGACATGTGTGGGGACG
* *
324369 AATCTATTACTCATCTTATTTAAGTACGAGAAATAAATACGTACAATTGGGTTTATAGTAGGCAA
1 AATCTATTACTCATCTTGTTTAAGTACGAGAAATAAATACCTACAATTGGGTTTATAGTAGGCAA
*
324434 AAAAGGCTAGAATAAAGAAGCACTATCAATAAACTTTACAAACAAATCTTGCATAAATTGGAAAG
66 GAAAGGCTAGAATAAAGAAGCACTATCAATAAACTTTACAAACAAATCTTGCATAAATTGGAAAG
* * *
324499 AAAATGACAATGAAAGTAAATGAAAATGAGAATAATGAACTAAGTATTTATAATAGAGTAAAAAT
131 AAAATGACAATGAAAGTGAATGAAAATGAGAATAAT--ACTAAGTATTTATAATGGAGTAAAAAA
324564 TATCTATGCACCAATTTCACTTTT
194 TATCTATGCACCAATTTCACTTTT
324588 GTCATCTTTA
Statistics
Matches: 713, Mismatches: 35, Indels: 10
0.94 0.05 0.01
Matches are distributed among these distances:
533 46 0.06
534 1 0.00
535 458 0.64
536 160 0.22
538 48 0.07
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.33
Consensus pattern (536 bp):
AATCTATTACTCATCTTGTTTAAGTACGAGAAATAAATACCTACAATTGGGTTTATAGTAGGCAA
GAAAGGCTAGAATAAAGAAGCACTATCAATAAACTTTACAAACAAATCTTGCATAAATTGGAAAG
AAAATGACAATGAAAGTGAATGAAAATGAGAATAATACTAAGTATTTATAATGGAGTAAAAAATA
TCTATGCACCAATTTCACTTTTTTTTTTTACATTCTGTCATATCATTAGTCAAATATTTTCTAGC
GTATCAGAAAGAATCTAATACCCACATGCGTTTATCACATCTTTCAGGTTCTAAAAAATTTATTA
GGTATTAGTCAAATATTTTTCGTCATGTCAAAAGGAATCTGTTGTCACATTTTTCAGGTTCCAAG
AAATTTATTAGGTATCAGTCAAATATTATCTATCGTGTCAGAAGGAATTTGATACCCACATGTGT
AGACACCTCATTTTGTCCAGACCAATTTTTGACAACTTGAGGCCTAGCTAGTAGGTGGAGGATTG
GACATGTGTGGGGACG
Found at i:324519 original size:16 final size:16
Alignment explanation
Indices: 324494--324527 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
324484 GCATAAATTG
*
324494 GAAAGAAAATGACAAT
1 GAAAGAAAATGAAAAT
*
324510 GAAAGTAAATGAAAAT
1 GAAAGAAAATGAAAAT
324526 GA
1 GA
324528 GAATAATGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.62, C:0.03, G:0.21, T:0.15
Consensus pattern (16 bp):
GAAAGAAAATGAAAAT
Found at i:344722 original size:15 final size:14
Alignment explanation
Indices: 344688--344730 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
344678 CGTCCTCCGC
344688 AAAAAAAAACAAAA
1 AAAAAAAAACAAAA
*
344702 AGAAAAAAAACACCAA
1 A-AAAAAAAACA-AAA
*
344718 AAAAAACAACAAA
1 AAAAAAAAACAAA
344731 CAGGGTCCGG
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
14 2 0.08
15 19 0.79
16 3 0.12
ACGTcount: A:0.84, C:0.14, G:0.02, T:0.00
Consensus pattern (14 bp):
AAAAAAAAACAAAA
Found at i:344732 original size:19 final size:18
Alignment explanation
Indices: 344688--344720 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
344678 CGTCCTCCGC
344688 AAAAAAAA-A-CAAAAAG
1 AAAAAAAACACCAAAAAG
344704 AAAAAAAACACCAAAAA
1 AAAAAAAACACCAAAAA
344721 AAACAACAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 8 0.53
17 1 0.07
18 6 0.40
ACGTcount: A:0.85, C:0.12, G:0.03, T:0.00
Consensus pattern (18 bp):
AAAAAAAACACCAAAAAG
Found at i:346211 original size:29 final size:28
Alignment explanation
Indices: 346165--346445 Score: 350
Period size: 29 Copynumber: 9.9 Consensus size: 28
346155 ATTTCTCACC
*
346165 TTTCAAAACCCACAAGTCAGTGGCATCT
1 TTTCAAAGCCCACAAGTCAGTGGCATCT
*
346193 TTTCAAAAGCCCACGAGTCAGTGGCA-CAT
1 TTTC-AAAGCCCACAAGTCAGTGGCATC-T
* *
346222 TTTCAAAGTCCACAAGTCAATGGCATCT
1 TTTCAAAGCCCACAAGTCAGTGGCATCT
* *
346250 TTTCAAAAGCGCACAAGTCAGTGGCACCCT
1 TTTC-AAAGCCCACAAGTCAGTGGCA-TCT
*
346280 TTTCAAAGCCCACAAGTCAGTAGCATCT
1 TTTCAAAGCCCACAAGTCAGTGGCATCT
*
346308 TTTCAAAGCACACAAGTCAGTGGCATCT
1 TTTCAAAGCCCACAAGTCAGTGGCATCT
*
346336 TTTCAAAAGCCCACAAGTCAGTGGCACCTT
1 TTTC-AAAGCCCACAAGTCAGTGGCATC-T
* *
346366 TTTCAAAGCCCATAAGTCAGTGGCACCT
1 TTTCAAAGCCCACAAGTCAGTGGCATCT
* *
346394 TTTCAAAGCCCATAAGTCAGTGGCAAC-
1 TTTCAAAGCCCACAAGTCAGTGGCATCT
* * *
346421 CTTCAAAGCCCACAAGGCAATGGCA
1 TTTCAAAGCCCACAAGTCAGTGGCA
346446 ACCTTCAAAA
Statistics
Matches: 224, Mismatches: 22, Indels: 15
0.86 0.08 0.06
Matches are distributed among these distances:
27 21 0.09
28 87 0.39
29 105 0.47
30 11 0.05
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.23
Consensus pattern (28 bp):
TTTCAAAGCCCACAAGTCAGTGGCATCT
Found at i:346253 original size:57 final size:57
Alignment explanation
Indices: 346165--346450 Score: 355
Period size: 57 Copynumber: 5.0 Consensus size: 57
346155 ATTTCTCACC
* * *
346165 TTTCAAAACCCACAAGTCAGTGGCATCTTTTCAAAAGCCCACGAGTCAGTGGCA-CAT
1 TTTCAAAGCCCACAAGTCAGTGGCATCTTTTC-AAAGCCCACAAGTCAGTGGCACCCT
* * *
346222 TTTCAAAGTCCACAAGTCAATGGCATCTTTTCAAAAGCGCACAAGTCAGTGGCACCCT
1 TTTCAAAGCCCACAAGTCAGTGGCATCTTTTC-AAAGCCCACAAGTCAGTGGCACCCT
* * *
346280 TTTCAAAGCCCACAAGTCAGTAGCATCTTTTCAAAGCACACAAGTCAGTGGCA-TCT
1 TTTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCACCCT
* *
346336 TTTCAAAAGCCCACAAGTCAGTGGCACCTTTTTCAAAGCCCATAAGTCAGTGGCA-CCT
1 TTTC-AAAGCCCACAAGTCAGTGGCATC-TTTTCAAAGCCCACAAGTCAGTGGCACCCT
* * * * * *
346394 TTTCAAAGCCCATAAGTCAGTGGCAAC-CTTCAAAGCCCACAAGGCAATGGCAACCT
1 TTTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCACCCT
346450 T
1 T
346451 CAAAAGCACA
Statistics
Matches: 203, Mismatches: 22, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
55 21 0.10
56 10 0.05
57 111 0.55
58 61 0.30
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.23
Consensus pattern (57 bp):
TTTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCACCCT
Found at i:346272 original size:86 final size:83
Alignment explanation
Indices: 346165--346450 Score: 362
Period size: 86 Copynumber: 3.4 Consensus size: 83
346155 ATTTCTCACC
* *
346165 TTTCAAAA-CCCACAAGTCAGTGGCATCTTTTCAAAAGCCCACGAGTCAGTGGCACATTTTCAAA
1 TTTCAAAAGCCCACAAGTCAGTGGCACCTTTTC-AAAGCCCACAAGTCAGTGGCAC-TTTTCAAA
*
346229 GTCCACAAGTCAATGGCATCT
64 G-CCACAAGTCAGTGGCATCT
* *
346250 TTTCAAAAGCGCACAAGTCAGTGGCACCCTTTTCAAAGCCCACAAGTCAGTAGCATCTTTTCAAA
1 TTTCAAAAGCCCACAAGTCAGTGGCA-CCTTTTCAAAGCCCACAAGTCAGTGGCA-CTTTTCAAA
346315 GCACACAAGTCAGTGGCATCT
64 GC-CACAAGTCAGTGGCATCT
*
346336 TTTCAAAAGCCCACAAGTCAGTGGCACCTTTTTCAAAGCCCATAAGTCAGTGGCACCTTTTCAAA
1 TTTCAAAAGCCCACAAGTCAGTGGCACC-TTTTCAAAGCCCACAAGTCAGTGGCA-CTTTTCAAA
* *
346401 GCCCATAAGTCAGTGGCAAC-
64 G-CCACAAGTCAGTGGCATCT
* * *
346421 CTTC-AAAGCCCACAAGGCAATGGCAACCTT
1 TTTCAAAAGCCCACAAGTCAGTGGC-ACCTT
346451 CAAAAGCACA
Statistics
Matches: 180, Mismatches: 14, Indels: 15
0.86 0.07 0.07
Matches are distributed among these distances:
84 20 0.11
85 17 0.09
86 135 0.75
87 8 0.04
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.23
Consensus pattern (83 bp):
TTTCAAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCACTTTTCAAAGC
CACAAGTCAGTGGCATCT
Found at i:346625 original size:49 final size:49
Alignment explanation
Indices: 346505--346993 Score: 513
Period size: 49 Copynumber: 9.9 Consensus size: 49
346495 GTTGGTGGCA
* * *
346505 TCATCTTTAAGTCCAATATCACTGGCCTTGAATCAGCATATTGG-----
1 TCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCT
* *
346549 T-AGCTTTAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGGCACCT
1 TCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCT
* * * *
346597 TCATCTTTAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGCACATTT
1 TCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCAC--CT
* *
346648 GTCATCTTTAAATCCAATGTCGCTGGCCTTGAATCAGCACATTAGCACCT
1 -TCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCT
* ** * *
346698 TCACCTTTAAGTCCAATGTTACTGGCCTTGAATCAGCATATTGGTACCT
1 TCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCT
* * * * *
346747 TTATCTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCATCTTT
1 TCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-C-CT
* *
346798 GTTATCTTTAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGGCACCT
1 -TCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCT
* * * *
346848 TCATCTTTAAGTCCAATATCGCTGGCTTTGAATCAGCATATTGGCACTTTT
1 TCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCAC--CT
** * *
346899 GTCATCTTTAAACCCAATGTCGCTGGCCTTGAATCAGCACATTAGCATTCT
1 -TCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-CCT
* * * * *
346950 CTCATCTTCAAGTCTAATGTCACTGACCGTGAATCAGCACATTG
1 -TCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTG
346994 ACATTCTTTA
Statistics
Matches: 373, Mismatches: 56, Indels: 25
0.82 0.12 0.06
Matches are distributed among these distances:
43 37 0.10
44 1 0.00
48 1 0.00
49 165 0.44
50 3 0.01
51 40 0.11
52 126 0.34
ACGTcount: A:0.25, C:0.24, G:0.17, T:0.34
Consensus pattern (49 bp):
TCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCT
Found at i:346727 original size:101 final size:101
Alignment explanation
Indices: 346505--347019 Score: 518
Period size: 101 Copynumber: 5.2 Consensus size: 101
346495 GTTGGTGGCA
* * * *
346505 TCATCTTTAAGTCCAATATCACTGGCCTTGAATCAGCATATTGG------T-AGCTTTAAGTCCA
1 TCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACTTTTCATCTTTAAGTCCA
*
346563 ATGTTGCTGGCCTTGAATCAGCACATTGGCAC-CT-
66 ATGTCGCTGGCCTTGAATCAGCACATTGGCACTCTG
* * * *
346597 TCATCTTTAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGCACATTTGTCATCTTTAAATC
1 TCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCAC-TTT-TCATCTTTAAGTC
*
346662 CAATGTCGCTGGCCTTGAATCAGCACATTAGCAC-CT-
64 CAATGTCGCTGGCCTTGAATCAGCACATTGGCACTCTG
* ** * * *
346698 TCACCTTTAAGTCCAATGTTACTGGCCTTGAATCAGCATATTGGTACCTTT-ATCTTTAAGTCCA
1 TCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACTTTTCATCTTTAAGTCCA
* * * *
346762 ATATTGCTGGCCTTGAATCAGCATATTGGCATCTTTG
66 ATGTCGCTGGCCTTGAATCAGCACATTGGCA-CTCTG
* * *
346799 TTATCTTTAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGGCAC-CTTCATCTTTAAGTCCA
1 TCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACTTTTCATCTTTAAGTCCA
* * * *
346863 ATATCGCTGGCTTTGAATCAGCATATTGGCACTTTTG
66 ATGTCGCTGGCCTTGAATCAGCACATTGGCAC-TCTG
** * *
346900 TCATCTTTAAACCCAATGTCGCTGGCCTTGAATCAGCACATTAGCA-TTCTCTCATCTTCAAGTC
1 TCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACTT-T-TCATCTTTAAGTC
* * * * * * *
346964 TAATGTCACTGACCGTGAATCAGCACATTGACATTCTT
64 CAATGTCGCTGGCCTTGAATCAGCACATTGGCACTCTG
*
347002 TACATCTTTAAGCCCAAT
1 T-CATCTTTAAGTCCAAT
347020 ATCACTGGTC
Statistics
Matches: 359, Mismatches: 46, Indels: 25
0.83 0.11 0.06
Matches are distributed among these distances:
92 42 0.12
98 39 0.11
99 2 0.01
100 7 0.02
101 213 0.59
102 4 0.01
103 52 0.14
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.34
Consensus pattern (101 bp):
TCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACTTTTCATCTTTAAGTCCA
ATGTCGCTGGCCTTGAATCAGCACATTGGCACTCTG
Found at i:346775 original size:150 final size:149
Alignment explanation
Indices: 346505--347056 Score: 591
Period size: 150 Copynumber: 3.7 Consensus size: 149
346495 GTTGGTGGCA
* * * * *
346505 TCATCTTTAAGTCCAATATCACTGGCCTTGAATCAGCATATTG----GT-AGCTTTAAGTCCAAT
1 TCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGCACCTTCATCTTTAAGTCCAAT
* ** * * *
346565 GTTGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTAGCCTTGAAT
66 ATCACTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATATCGCTGGCCTTGAAT
346630 CAGCATATTGGCACATTTG
131 CAGCATATTGGCACATTTG
* *
346649 TCATCTTTAAATCCAATGTCGCTGGCCTTGAATCAGCACATTAGCACCTTCACCTTTAAGTCCAA
1 TCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATT-GCACCTTCATCTTTAAGTCCAA
* * * *
346714 TGTTACTGGCCTTGAATCAGCATATTGGTACCTTTATCTTTAAGTCCAATATTGCTGGCCTTGAA
65 TATCACTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATATCGCTGGCCTTGAA
346779 TCAGCATATTGGCATC-TTTG
130 TCAGCATATTGGCA-CATTTG
* *
346799 TTATCTTTAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAA
1 TCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATT-GCACCTTCATCTTTAAGTCCAA
* * * ** *
346864 TATCGCTGGCTTTGAATCAGCATATTGGCACTTTTGTCATCTTTAAACCCAATGTCGCTGGCCTT
65 TATCACTGGCCTTGAATCAGCATATTGGCAC-CTT-T-ATCTTTAAGTCCAATATCGCTGGCCTT
* * *
346929 GAATCAGCACATTAG--CATTCTC
127 GAATCAGCATATTGGCACATT-TG
* * * * * * *
346951 TCATCTTCAAGTCTAATGTCACTGACCGTGAATCAGCACATTGACATTCTTTACATCTTTAAGCC
1 TCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTG-CA--CCTT-CATCTTTAAGTC
* * *
347016 CAATATCACTGGTCC-TCAATCAGCATGTTGGTACCTTTATC
62 CAATATCACTGG-CCTTGAATCAGCATATTGGCACCTTTATC
347057 ACTCTTCTCA
Statistics
Matches: 346, Mismatches: 45, Indels: 26
0.83 0.11 0.06
Matches are distributed among these distances:
144 38 0.11
145 1 0.00
149 1 0.00
150 177 0.51
151 6 0.02
152 42 0.12
153 37 0.11
154 5 0.01
155 38 0.11
156 1 0.00
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.34
Consensus pattern (149 bp):
TCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGCACCTTCATCTTTAAGTCCAAT
ATCACTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATATCGCTGGCCTTGAAT
CAGCATATTGGCACATTTG
Found at i:347037 original size:52 final size:51
Alignment explanation
Indices: 346569--347040 Score: 261
Period size: 52 Copynumber: 9.3 Consensus size: 51
346559 TCCAATGTTG
* * * * *
346569 CTGGCCTTGAATCAGCACATTGGCA--CCTTCATCTTTAAGTCCAATATCG
1 CTGGCCGTGAATCAGCACATTGACATTCTTTCATCTTTAAGCCCAATATCA
* * * * ** * *
346618 CTAGCCTTGAATCAGCATATTGGCACATT-TGTCATCTTTAAATCCAATGTCG
1 CTGGCCGTGAATCAGCACATT-G-ACATTCTTTCATCTTTAAGCCCAATATCA
* * * * * *
346670 CTGGCCTTGAATCAGCACATT-AGCA--CCTTCACCTTTAAGTCCAATGTTA
1 CTGGCCGTGAATCAGCACATTGA-CATTCTTTCATCTTTAAGCCCAATATCA
* * ** * * **
346719 CTGGCCTTGAATCAGCATATTGGTA-CCTTT-ATCTTTAAGTCCAATATTG
1 CTGGCCGTGAATCAGCACATTGACATTCTTTCATCTTTAAGCCCAATATCA
* * * * * * **
346768 CTGGCCTTGAATCAGCATATTGGCA-TCTTTGTTATCTTTAAGTCCAATGTTG
1 CTGGCCGTGAATCAGCACATTGACATTC-TT-TCATCTTTAAGCCCAATATCA
* * * * *
346820 CTGGCCTTGAATCAGCACATTGGCA--CCTTCATCTTTAAGTCCAATATCG
1 CTGGCCGTGAATCAGCACATTGACATTCTTTCATCTTTAAGCCCAATATCA
** * * * * *
346869 CTGGCTTTGAATCAGCATATTGGCACTT-TTGTCATCTTTAAACCCAATGTCG
1 CTGGCCGTGAATCAGCACATTGACA-TTCTT-TCATCTTTAAGCCCAATATCA
* * * * * *
346921 CTGGCCTTGAATCAGCACATT-AGCATTCTCTCATCTTCAAGTCTAATGTCA
1 CTGGCCGTGAATCAGCACATTGA-CATTCTTTCATCTTTAAGCCCAATATCA
*
346972 CTGACCGTGAATCAGCACATTGACATTCTTTACATCTTTAAGCCCAATATCA
1 CTGGCCGTGAATCAGCACATTGACATTCTTT-CATCTTTAAGCCCAATATCA
*
347024 CTGGTCC-TCAATCAGCA
1 CTGG-CCGTGAATCAGCA
347041 TGTTGGTACC
Statistics
Matches: 349, Mismatches: 54, Indels: 37
0.79 0.12 0.08
Matches are distributed among these distances:
49 140 0.40
50 9 0.03
51 49 0.14
52 149 0.43
53 2 0.01
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.34
Consensus pattern (51 bp):
CTGGCCGTGAATCAGCACATTGACATTCTTTCATCTTTAAGCCCAATATCA
Found at i:351114 original size:89 final size:89
Alignment explanation
Indices: 350991--351373 Score: 541
Period size: 89 Copynumber: 4.3 Consensus size: 89
350981 CGTTGCGACA
* * * **
350991 ACATGCATCTGTCAGATTTTTCGGGTTCCAAGAAATTTATGAGATATTAGTCAAATATTTTTCGT
1 ACATGCATCTGTCACATCTTTCGGGTTCCAAGAAATTTATTAGGCATTAGTCAAATATTTTTCGT
* *
351056 CATGTCAGAAGGAATCTGATACCG
66 CGTGTCAGAAGGAATCTGATACCC
* **
351080 ACATGCATCTGTCACATCTTTCGAGTTTTAAGAAATTTATTAGGCATTAGTCAAATATTTTTCGT
1 ACATGCATCTGTCACATCTTTCGGGTTCCAAGAAATTTATTAGGCATTAGTCAAATATTTTTCGT
*
351145 CTTGTCAGAAGGAATCTGATACCC
66 CGTGTCAGAAGGAATCTGATACCC
* *
351169 ACATGCATCTGTCACATCTTTCGGGTTCCAAGAAATTTATTAGGCATTAGTCAAATATTTTCCAT
1 ACATGCATCTGTCACATCTTTCGGGTTCCAAGAAATTTATTAGGCATTAGTCAAATATTTTTCGT
* *
351234 CGTGTCAGAAAGAATTTGATACCC
66 CGTGTCAGAAGGAATCTGATACCC
** * *
351258 ACATGCATCTGTCACATCTTTCAAGTTCCAAAAAATTTATTAGGCATTAGTCAAATATTTTTCTT
1 ACATGCATCTGTCACATCTTTCGGGTTCCAAGAAATTTATTAGGCATTAGTCAAATATTTTTCGT
* * * *
351323 TGTGTCAAAAGGGATCTGATACAC
66 CGTGTCAGAAGGAATCTGATACCC
* *
351347 ATATGCATCTATCACATCTTTCGGGTT
1 ACATGCATCTGTCACATCTTTCGGGTT
351374 TTAAAAAAAT
Statistics
Matches: 261, Mismatches: 33, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
89 261 1.00
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36
Consensus pattern (89 bp):
ACATGCATCTGTCACATCTTTCGGGTTCCAAGAAATTTATTAGGCATTAGTCAAATATTTTTCGT
CGTGTCAGAAGGAATCTGATACCC
Found at i:351719 original size:15 final size:15
Alignment explanation
Indices: 351699--351752 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
351689 TATCGTTGGT
351699 GCTTCTTCCTGAATG
1 GCTTCTTCCTGAATG
* *
351714 GCTTCTT-CTTAAGTA
1 GCTTCTTCCTGAA-TG
* *
351729 GCTTCTTCTTGAGTG
1 GCTTCTTCCTGAATG
351744 GCTTCTTCC
1 GCTTCTTCC
351753 GGGTGGTTTC
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
14 4 0.13
15 24 0.80
16 2 0.07
ACGTcount: A:0.11, C:0.26, G:0.19, T:0.44
Consensus pattern (15 bp):
GCTTCTTCCTGAATG
Found at i:353817 original size:21 final size:21
Alignment explanation
Indices: 353791--353844 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
353781 TTCATCGTAC
*
353791 TAAAATTATACTTAATTAGAA
1 TAAAATTATACTTAATCAGAA
*
353812 TAAAATT-TAATTTAATCAGAA
1 TAAAATTAT-ACTTAATCAGAA
353833 TAATAAATTATA
1 T-A-AAATTATA
353845 AAGTTAATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
20 1 0.04
21 18 0.67
22 1 0.04
23 6 0.22
24 1 0.04
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.39
Consensus pattern (21 bp):
TAAAATTATACTTAATCAGAA
Found at i:354488 original size:2 final size:2
Alignment explanation
Indices: 354481--354513 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
354471 TAACCCACTT
354481 TA 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 TA T
354514 TATTAATGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:354667 original size:16 final size:14
Alignment explanation
Indices: 354637--354703 Score: 72
Period size: 14 Copynumber: 5.0 Consensus size: 14
354627 AAGTTAATAA
354637 TATAACATATATTT
1 TATAACATATATTT
354651 TATAACATA-ACTATT
1 TATAACATATA-T-TT
354666 T-TAA-A-A-ATTT
1 TATAACATATATTT
354676 TATAACATATATTT
1 TATAACATATATTT
*
354690 TATAAAATATATTT
1 TATAACATATATTT
354704 AAAAATAAAT
Statistics
Matches: 46, Mismatches: 1, Indels: 12
0.78 0.02 0.20
Matches are distributed among these distances:
10 3 0.07
11 4 0.09
12 3 0.07
13 3 0.07
14 30 0.65
15 3 0.07
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (14 bp):
TATAACATATATTT
Found at i:354675 original size:25 final size:24
Alignment explanation
Indices: 354647--354697 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 24
354637 TATAACATAT
354647 ATTTTATAACATAACTATTTTA-AAA
1 ATTTTATAACAT-A-TATTTTATAAA
354672 ATTTTATAACATATATTTTATAAA
1 ATTTTATAACATATATTTTATAAA
354696 AT
1 AT
354698 ATATTTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
23 7 0.28
24 6 0.24
25 12 0.48
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (24 bp):
ATTTTATAACATATATTTTATAAA
Found at i:354691 original size:39 final size:36
Alignment explanation
Indices: 354637--354709 Score: 110
Period size: 39 Copynumber: 1.9 Consensus size: 36
354627 AAGTTAATAA
*
354637 TATAACATATATTTTATAACATAACTATTTTAAAAATTT
1 TATAACATATATTTTATAAAAT-A-TA-TTTAAAAATTT
354676 TATAACATATATTTTATAAAATATATTTAAAAAT
1 TATAACATATATTTTATAAAATATATTTAAAAAT
354710 AAATAAAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
36 9 0.27
37 2 0.06
38 1 0.03
39 21 0.64
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.45
Consensus pattern (36 bp):
TATAACATATATTTTATAAAATATATTTAAAAATTT
Found at i:355296 original size:185 final size:183
Alignment explanation
Indices: 354984--355351 Score: 574
Period size: 185 Copynumber: 2.0 Consensus size: 183
354974 AAATTAAAAC
* * * * *
354984 TAATTATACCTTAGTTGGTAATAACGAAAAACTTAATTATAGTAAAATTAAATTTAATCATAACA
1 TAATTATACCTTAGTTAGCAATAACAAAAAACTTAATTACAATAAAATTAAATTTAATCATAACA
* * *
355049 ATAAATTACAAAATGAATTATATTTCAAGATTATAAGAATACTTATAGAAATAAAAATAAAACAT
66 ATAAATTACAAAACGAATTATATTTCAAAATTATAACAATACTTATAGAAATAAAAATAAAACAT
* * *
355114 ACCTTCAAAATTATTATATAATCCGAACAAAATTTTTTTCTATAACAACACAAAT
131 ACCTTCAAAATTATTATATAACCCAAAC-AAATTTTTTT-AATAACAACACAAAT
355169 TAATTATACCTTAGTTAGCAATAACAAAAAACTTAATTACAATAAAATTAAATTTAATCATAACA
1 TAATTATACCTTAGTTAGCAATAACAAAAAACTTAATTACAATAAAATTAAATTTAATCATAACA
* *
355234 ATAAATTATAAAACGAATTATATTTCAAAATTATAACAATACTTATATAAATAAAAATAAAACAT
66 ATAAATTACAAAACGAATTATATTTCAAAATTATAACAATACTTATAGAAATAAAAATAAAACAT
* * *
355299 ACCTTTAAAATTTTTATATAACCCAAACAAATTTTTTTAATAACAATACAAAT
131 ACCTTCAAAATTATTATATAACCCAAACAAATTTTTTTAATAACAACACAAAT
355352 ATAAATTTTA
Statistics
Matches: 167, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
183 13 0.08
184 10 0.06
185 144 0.86
ACGTcount: A:0.52, C:0.11, G:0.04, T:0.34
Consensus pattern (183 bp):
TAATTATACCTTAGTTAGCAATAACAAAAAACTTAATTACAATAAAATTAAATTTAATCATAACA
ATAAATTACAAAACGAATTATATTTCAAAATTATAACAATACTTATAGAAATAAAAATAAAACAT
ACCTTCAAAATTATTATATAACCCAAACAAATTTTTTTAATAACAACACAAAT
Found at i:355884 original size:11 final size:11
Alignment explanation
Indices: 355865--355903 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
355855 AGTTCTCACC
*
355865 TAAAAAAATTT
1 TAAAAAAATTA
*
355876 TAAATAAATTA
1 TAAAAAAATTA
355887 TAAAAAAATTA
1 TAAAAAAATTA
355898 -AAAAAA
1 TAAAAAA
355904 TGGAAAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
10 6 0.24
11 19 0.76
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
TAAAAAAATTA
Found at i:355898 original size:20 final size:21
Alignment explanation
Indices: 355865--355904 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
355855 AGTTCTCACC
*
355865 TAAAAAAATTTTAAATAAATTA
1 TAAAAAAA-TTTAAAAAAATTA
355887 TAAAAAAA-TTAAAAAAAT
1 TAAAAAAATTTAAAAAAAT
355905 GGAAAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
22 8 0.47
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (21 bp):
TAAAAAAATTTAAAAAAATTA
Found at i:360804 original size:22 final size:22
Alignment explanation
Indices: 360779--360834 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
360769 TTCAGATATA
360779 TAATAATATCTCA-TTTATTTTT
1 TAATAATAT-TCATTTTATTTTT
* *
360801 TAATATTATTTATTTTTATTTTT
1 TAATAATATTCA-TTTTATTTTT
*
360824 TAATAAAATTC
1 TAATAATATTC
360835 TAATAAAATA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
21 2 0.07
22 8 0.30
23 17 0.63
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (22 bp):
TAATAATATTCATTTTATTTTT
Found at i:361971 original size:21 final size:21
Alignment explanation
Indices: 361937--361983 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
361927 TATGTATACA
*
361937 ATATA-TATATATACATAAAT
1 ATATACTATACATACATAAAT
*
361957 ATATACTATACATACATACAT
1 ATATACTATACATACATAAAT
*
361978 ACATAC
1 ATATAC
361984 GGTAGTGGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.51, C:0.15, G:0.00, T:0.34
Consensus pattern (21 bp):
ATATACTATACATACATAAAT
Found at i:367106 original size:14 final size:14
Alignment explanation
Indices: 367087--367117 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
367077 TTTTAAGAGC
367087 ATTCAATTAGATCT
1 ATTCAATTAGATCT
367101 ATTCAATTAGATCT
1 ATTCAATTAGATCT
367115 ATT
1 ATT
367118 TATGGATCAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.45
Consensus pattern (14 bp):
ATTCAATTAGATCT
Found at i:369086 original size:2 final size:2
Alignment explanation
Indices: 369079--369120 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
369069 TAGGCCATGC
369079 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
369121 TTACCGATAT
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:371001 original size:9 final size:9
Alignment explanation
Indices: 370987--371015 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
370977 ATGAGTTTGA
370987 AAAATTAGG
1 AAAATTAGG
370996 AAAATTAGG
1 AAAATTAGG
371005 -AAATTAGG
1 AAAATTAGG
371013 AAA
1 AAA
371016 CAATCCTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.59, C:0.00, G:0.21, T:0.21
Consensus pattern (9 bp):
AAAATTAGG
Found at i:371731 original size:15 final size:15
Alignment explanation
Indices: 371713--371828 Score: 78
Period size: 15 Copynumber: 7.6 Consensus size: 15
371703 AATTATGAAG
371713 AAATAAATTGCAAGA
1 AAATAAATTGCAAGA
*
371728 AAATAAATTACATA-A
1 AAATAAATTGCA-AGA
** *
371743 ATTTAAATTGCAAAA
1 AAATAAATTGCAAGA
371758 AAATAAATTGCATA-A
1 AAATAAATTGCA-AGA
*
371773 ATTAA-AAATTGCAAGG
1 A--AATAAATTGCAAGA
*
371789 AAATAAATTG-AATA
1 AAATAAATTGCAAGA
* *
371803 AATTGAAAATTTCAAGA
1 AAAT--AAATTGCAAGA
371820 AAATAAATT
1 AAATAAATT
371829 AACTACATGA
Statistics
Matches: 78, Mismatches: 13, Indels: 20
0.70 0.12 0.18
Matches are distributed among these distances:
14 8 0.10
15 46 0.59
16 16 0.21
17 8 0.10
ACGTcount: A:0.59, C:0.05, G:0.09, T:0.28
Consensus pattern (15 bp):
AAATAAATTGCAAGA
Found at i:371737 original size:30 final size:30
Alignment explanation
Indices: 371701--371829 Score: 97
Period size: 31 Copynumber: 4.2 Consensus size: 30
371691 TGCATAAATT
*
371701 TAAATTATGAAGAAATAAATTGCAAGAAAA
1 TAAATTATGAATAAATAAATTGCAAGAAAA
* *
371731 TAAATTA--CATAAATTTAAATTGCAAAAAAA
1 TAAATTATGAATAAA--TAAATTGCAAGAAAA
* * *
371761 TAAATTGCATAAATTAA-AAATTGCAAGGAAA
1 TAAATT--ATGAATAAATAAATTGCAAGAAAA
*
371792 TAAA-T-TGAATAAATTGAAAATTTCAAGAAAA
1 TAAATTATGAATAAA-T--AAATTGCAAGAAAA
371823 TAAATTA
1 TAAATTA
371830 ACTACATGAT
Statistics
Matches: 76, Mismatches: 11, Indels: 21
0.70 0.10 0.19
Matches are distributed among these distances:
27 6 0.08
28 4 0.05
30 28 0.37
31 32 0.42
32 2 0.03
34 4 0.05
ACGTcount: A:0.58, C:0.05, G:0.09, T:0.28
Consensus pattern (30 bp):
TAAATTATGAATAAATAAATTGCAAGAAAA
Found at i:371742 original size:45 final size:46
Alignment explanation
Indices: 371670--371769 Score: 130
Period size: 45 Copynumber: 2.2 Consensus size: 46
371660 TTGTATAGAT
* ** *
371670 TAAATTGCAACAAAAGTAAAGTGCATAAATTTAAATTATGAAGAAA
1 TAAATTGCAACAAAAGTAAAGTACATAAATTTAAATTACAAAAAAA
* * *
371716 TAAATTGCAAGAAAA-TAAATTACATAAATTTAAATTGCAAAAAAA
1 TAAATTGCAACAAAAGTAAAGTACATAAATTTAAATTACAAAAAAA
371761 TAAATTGCA
1 TAAATTGCA
371770 TAAATTAAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
45 33 0.70
46 14 0.30
ACGTcount: A:0.56, C:0.07, G:0.10, T:0.27
Consensus pattern (46 bp):
TAAATTGCAACAAAAGTAAAGTACATAAATTTAAATTACAAAAAAA
Found at i:371785 original size:31 final size:30
Alignment explanation
Indices: 371717--371828 Score: 152
Period size: 31 Copynumber: 3.7 Consensus size: 30
371707 ATGAAGAAAT
* *
371717 AAATTGCAAGAAAATAAATTACATAAATTT
1 AAATTGCAAGAAAATAAATTGCATAAATTA
*
371747 AAATTGCAAAAAAATAAATTGCATAAATTAA
1 AAATTGCAAGAAAATAAATTGCATAAATT-A
* *
371778 AAATTGCAAGGAAATAAATTGAATAAATTGA
1 AAATTGCAAGAAAATAAATTGCATAAATT-A
*
371809 AAATTTCAAGAAAATAAATT
1 AAATTGCAAGAAAATAAATT
371829 AACTACATGA
Statistics
Matches: 72, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
30 27 0.38
31 45 0.62
ACGTcount: A:0.58, C:0.05, G:0.09, T:0.28
Consensus pattern (30 bp):
AAATTGCAAGAAAATAAATTGCATAAATTA
Found at i:373480 original size:21 final size:21
Alignment explanation
Indices: 373456--373495 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
373446 TTTGAAATAT
373456 ATTTATTATTAACAAACATTA
1 ATTTATTATTAACAAACATTA
*
373477 ATTTATTGTTAACAAACAT
1 ATTTATTATTAACAAACAT
373496 GTCATATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.45, C:0.10, G:0.03, T:0.42
Consensus pattern (21 bp):
ATTTATTATTAACAAACATTA
Found at i:390721 original size:21 final size:21
Alignment explanation
Indices: 390700--390738 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
390690 TCTAAACAGC
390700 CCAT-TTTCATGCATTTTAAG
1 CCATGTTTCATGCATTTTAAG
*
390720 CCATGTTTCGTGCATTTTA
1 CCATGTTTCATGCATTTTA
390739 GCATGTCTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.21, C:0.21, G:0.13, T:0.46
Consensus pattern (21 bp):
CCATGTTTCATGCATTTTAAG
Found at i:393276 original size:27 final size:27
Alignment explanation
Indices: 393233--393286 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
393223 GGGTTAATCT
*
393233 TAAAATTCAAAGTTAATACTATT-TTAA
1 TAAAATTCAAAGATAATA-TATTATTAA
393260 TAAAATT-AAAGGATAATATATTATTAA
1 TAAAATTCAAA-GATAATATATTATTAA
393287 ATATAATCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 7 0.29
27 17 0.71
ACGTcount: A:0.52, C:0.04, G:0.06, T:0.39
Consensus pattern (27 bp):
TAAAATTCAAAGATAATATATTATTAA
Found at i:395737 original size:17 final size:17
Alignment explanation
Indices: 395715--395778 Score: 76
Period size: 17 Copynumber: 3.7 Consensus size: 17
395705 TTAAAATATT
395715 ATTTATTATTTTTAAAA
1 ATTTATTATTTTTAAAA
* * *
395732 ATTTATTGTTTATCTTAAT
1 ATTTATTATTT-T-TAAAA
395751 ATTTATTATTTTTAAAA
1 ATTTATTATTTTTAAAA
395768 ATTTATT-TTTT
1 ATTTATTATTTT
395779 ATCTTAACTT
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
16 4 0.10
17 20 0.51
18 2 0.05
19 13 0.33
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (17 bp):
ATTTATTATTTTTAAAA
Found at i:395737 original size:21 final size:21
Alignment explanation
Indices: 395707--395780 Score: 63
Period size: 21 Copynumber: 3.8 Consensus size: 21
395697 ATGTATATTT
395707 AAAATATTATTTATTATTTTTA
1 AAAAT-TTATTTATTATTTTTA
*
395729 AAAATTTATTGT-TTA-TCTT-
1 AAAATTTATT-TATTATTTTTA
395748 --AA--TATTTATTATTTTTA
1 AAAATTTATTTATTATTTTTA
*
395765 AAAATTTATTTTTTAT
1 AAAATTTATTTATTAT
395781 CTTAACTTAC
Statistics
Matches: 41, Mismatches: 3, Indels: 17
0.67 0.05 0.28
Matches are distributed among these distances:
14 1 0.02
15 7 0.17
16 3 0.07
17 2 0.05
19 2 0.05
20 3 0.07
21 17 0.41
22 6 0.15
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.61
Consensus pattern (21 bp):
AAAATTTATTTATTATTTTTA
Found at i:395759 original size:36 final size:36
Alignment explanation
Indices: 395714--395785 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
395704 TTTAAAATAT
395714 TATTTATTATTTTTAAAAATTTATTGTTTATCTTAA
1 TATTTATTATTTTTAAAAATTTATTGTTTATCTTAA
*
395750 TATTTATTATTTTTAAAAATTTATTTTTTATCTTAA
1 TATTTATTATTTTTAAAAATTTATTGTTTATCTTAA
395786 CTTACCATGT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.62
Consensus pattern (36 bp):
TATTTATTATTTTTAAAAATTTATTGTTTATCTTAA
Found at i:396442 original size:19 final size:18
Alignment explanation
Indices: 396423--396458 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
396413 AATAATTTAT
*
396423 TTTAATAAAAAATTAATA
1 TTTAATAAAAAATAAATA
*
396441 TTTCATAAAAAATAAATA
1 TTTAATAAAAAATAAATA
396459 GATGAAAATT
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:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (18 bp):
TTTAATAAAAAATAAATA
Found at i:400712 original size:13 final size:13
Alignment explanation
Indices: 400694--400721 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
400684 ATACAAAGGT
400694 CAATGTATCGATA
1 CAATGTATCGATA
400707 CAATGTATCGATA
1 CAATGTATCGATA
400720 CA
1 CA
400722 TTTGAGTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:400796 original size:15 final size:15
Alignment explanation
Indices: 400776--400808 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
400766 CGATACATTG
400776 TATCGATACAACACT
1 TATCGATACAACACT
400791 TATCGATACAACACT
1 TATCGATACAACACT
400806 TAT
1 TAT
400809 GTATCGATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.39, C:0.24, G:0.06, T:0.30
Consensus pattern (15 bp):
TATCGATACAACACT
Found at i:400815 original size:19 final size:16
Alignment explanation
Indices: 400774--400819 Score: 58
Period size: 15 Copynumber: 2.8 Consensus size: 16
400764 AGCGATACAT
400774 TGTATCGATACAACAC
1 TGTATCGATACAACAC
400790 T-TATCGATACAACAC
1 TGTATCGATACAACAC
400805 TTATGTATCGATACA
1 ---TGTATCGATACA
400820 GTTACTTGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
15 14 0.54
16 1 0.04
18 1 0.04
19 10 0.38
ACGTcount: A:0.37, C:0.22, G:0.11, T:0.30
Consensus pattern (16 bp):
TGTATCGATACAACAC
Found at i:403798 original size:32 final size:33
Alignment explanation
Indices: 403710--403798 Score: 90
Period size: 36 Copynumber: 2.6 Consensus size: 33
403700 CAATGTATAA
* *
403710 ATTAATTAAATTTAAAAAATTTAATAAATAATAT
1 ATTAATTAAATTTAAAAAA-TAAAAAAATAATAT
* *
403744 ATTAATTATTATTTTTATAAAATAAAAAAATAATAT
1 ATTAATTA--A-ATTTAAAAAATAAAAAAATAATAT
*
403780 -TTAATTAAGTTTAAAAAAT
1 ATTAATTAAATTTAAAAAAT
403799 TGAGGTATGA
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
32 9 0.20
33 1 0.02
34 8 0.17
35 7 0.15
36 13 0.28
37 8 0.17
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (33 bp):
ATTAATTAAATTTAAAAAATAAAAAAATAATAT
Found at i:406326 original size:15 final size:15
Alignment explanation
Indices: 406306--406334 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
406296 TATATAATAA
406306 AATAAAAATAAATTT
1 AATAAAAATAAATTT
406321 AATAAAAATAAATT
1 AATAAAAATAAATT
406335 AAATTAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
AATAAAAATAAATTT
Found at i:406337 original size:20 final size:24
Alignment explanation
Indices: 406289--406339 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 24
406279 AATTAATATT
406289 TTAAATTTATATAATAAAATAAAA
1 TTAAATTTATATAATAAAATAAAA
*
406313 ATAAATTTA-AT-A-AAAAT-AAA
1 TTAAATTTATATAATAAAATAAAA
406333 TTAAATT
1 TTAAATT
406340 AATTTTATAG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 9 0.36
21 5 0.20
22 1 0.04
23 2 0.08
24 8 0.32
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (24 bp):
TTAAATTTATATAATAAAATAAAA
Found at i:408808 original size:18 final size:18
Alignment explanation
Indices: 408787--408824 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
408777 GAAATGAGAT
408787 TTCTAAATGAAAG-TAATA
1 TTCTAAA-GAAAGTTAATA
*
408805 TTCTCAAGAAAGTTAATA
1 TTCTAAAGAAAGTTAATA
408823 TT
1 TT
408825 TTATTGCATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.45, C:0.08, G:0.11, T:0.37
Consensus pattern (18 bp):
TTCTAAAGAAAGTTAATA
Found at i:408971 original size:15 final size:15
Alignment explanation
Indices: 408953--408981 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
408943 ATTAAAAGAA
408953 AACAATAATAATAAT
1 AACAATAATAATAAT
408968 AACAATAATAATAA
1 AACAATAATAATAA
408982 CAAACAACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (15 bp):
AACAATAATAATAAT
Found at i:408976 original size:12 final size:12
Alignment explanation
Indices: 408959--408984 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
408949 AGAAAACAAT
408959 AATAATAATAAC
1 AATAATAATAAC
408971 AATAATAATAAC
1 AATAATAATAAC
408983 AA
1 AA
408985 ACAACCATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (12 bp):
AATAATAATAAC
Found at i:409728 original size:21 final size:21
Alignment explanation
Indices: 409702--409742 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
409692 TGTTTAAAAT
409702 TTTTAAATAC-AATATTTATAA
1 TTTTAAA-ACTAATATTTATAA
*
409723 TTTTAAAACTTATATTTATA
1 TTTTAAAACTAATATTTATA
409743 TATAAACATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (21 bp):
TTTTAAAACTAATATTTATAA
Found at i:409754 original size:18 final size:18
Alignment explanation
Indices: 409728--409764 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
409718 TATAATTTTA
* *
409728 AAACTTATATTTATATAT
1 AAACATATATATATATAT
409746 AAACATATATATATATAT
1 AAACATATATATATATAT
409764 A
1 A
409765 TATTAGAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.43
Consensus pattern (18 bp):
AAACATATATATATATAT
Found at i:412904 original size:50 final size:49
Alignment explanation
Indices: 412829--413010 Score: 197
Period size: 50 Copynumber: 3.7 Consensus size: 49
412819 TCACAATTTA
*
412829 TATCGATACATTCTTCATTGTATCGATACATTTTAGGTTTTACCCAGATG
1 TATCGATACATTCTTCATTGTATCGATACATTAT-GGTTTTACCCAGATG
* * * * *
412879 TATCGACACATTCTTTATTGTATCGATACATTCTGAGTTTTACCCAAATA
1 TATCGATACATTCTTCATTGTATCGATACATTATG-GTTTTACCCAGATG
*
412929 TATCGATACATT-TCTCATTGCATCGATACATTATGGGTTTTACCCAGATG
1 TATCGATACATTCT-TCATTGTATCGATACATTAT-GGTTTTACCCAGATG
* * * * *
412979 CATTGATATATT-TCTCAATGTATTGATACATT
1 TATCGATACATTCT-TCATTGTATCGATACATT
413011 CAGGTAGTTT
Statistics
Matches: 112, Mismatches: 17, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
49 2 0.02
50 109 0.97
51 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.41
Consensus pattern (49 bp):
TATCGATACATTCTTCATTGTATCGATACATTATGGTTTTACCCAGATG
Found at i:413001 original size:100 final size:100
Alignment explanation
Indices: 412827--413011 Score: 248
Period size: 100 Copynumber: 1.9 Consensus size: 100
412817 TTTCACAATT
* * *
412827 TATATCGATACATTCTTCATTGTATCGATACATTTTAGGTTTTACCCAGATGTATCGACACATTC
1 TATATCGATACATTCTTCATTGCATCGATACATTATAGGTTTTACCCAGATGCATCGACACATTC
* *
412892 TTTATTGTATCGATACATTCTGAGTTTTACCCAAA
66 TTCAATGTATCGATACATTCTGAGTTTTACCCAAA
* * * *
412927 TATATCGATACATT-TCTCATTGCATCGATACATTATGGGTTTTACCCAGATGCATTGATATATT
1 TATATCGATACATTCT-TCATTGCATCGATACATTATAGGTTTTACCCAGATGCATCGACACATT
*
412991 -TCTCAATGTATTGATACATTC
65 CT-TCAATGTATCGATACATTC
413012 AGGTAGTTTT
Statistics
Matches: 73, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
99 2 0.03
100 71 0.97
ACGTcount: A:0.28, C:0.18, G:0.12, T:0.41
Consensus pattern (100 bp):
TATATCGATACATTCTTCATTGCATCGATACATTATAGGTTTTACCCAGATGCATCGACACATTC
TTCAATGTATCGATACATTCTGAGTTTTACCCAAA
Found at i:415217 original size:79 final size:76
Alignment explanation
Indices: 415035--415236 Score: 239
Period size: 75 Copynumber: 2.6 Consensus size: 76
415025 CGATTTTCTG
* * * *
415035 CCATCGGGGATACTCCAATCCCGTTATTTTTGAGAAGATACTCCAA-CCCTTTTTTTTTAAAACA
1 CCATCGGGGATACTCCAACCCCGTTATTTTCGAGGAGATACTCCAACCCCTTTTTTTTCAAAACA
*
415099 TCGATTTTCCA
66 TCAATTTTCCA
** * *
415110 TAATCGGGGATACAT-CAACCCTGTTATTTTCGAGGGGATACTCCAACCCCGTTTTATTTTCAAA
1 CCATCGGGGATAC-TCCAACCCCGTTATTTTCGAGGAGATACTCCAACCCC-TTTT-TTTTCAAA
*
415174 ACATCAATTTTTCA
63 ACATCAATTTTCCA
*
415188 CCATCGGCGAATACTCCAACCCCGTTA-TTTCTGAGGAGATACTCCAACC
1 CCATCGG-GGATACTCCAACCCCGTTATTTTC-GAGGAGATACTCCAACC
415237 TCATTTTTAT
Statistics
Matches: 105, Mismatches: 15, Indels: 10
0.81 0.12 0.08
Matches are distributed among these distances:
75 37 0.35
76 4 0.04
77 4 0.04
78 29 0.28
79 31 0.30
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.32
Consensus pattern (76 bp):
CCATCGGGGATACTCCAACCCCGTTATTTTCGAGGAGATACTCCAACCCCTTTTTTTTCAAAACA
TCAATTTTCCA
Found at i:420429 original size:20 final size:19
Alignment explanation
Indices: 420400--420438 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
420390 AGGTCAAAAC
420400 CCTTAAATGTATCGATACA
1 CCTTAAATGTATCGATACA
420419 CCTTCAAATGTATCGATACA
1 CCTT-AAATGTATCGATACA
420439 TAATGCACAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.36, C:0.23, G:0.10, T:0.31
Consensus pattern (19 bp):
CCTTAAATGTATCGATACA
Found at i:420485 original size:20 final size:21
Alignment explanation
Indices: 420460--420512 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
420450 ATCCATACAT
*
420460 TGTATCGATACATG-ACCA-AA
1 TGTATCGATACATGCA-AAGAA
*
420480 TGTATCGATACTTGCAAAGAA
1 TGTATCGATACATGCAAAGAA
420501 TGTATCGATACA
1 TGTATCGATACA
420513 GGTGCTTGGT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (21 bp):
TGTATCGATACATGCAAAGAA
Found at i:426751 original size:13 final size:13
Alignment explanation
Indices: 426733--426835 Score: 134
Period size: 13 Copynumber: 7.9 Consensus size: 13
426723 TAGCATTCTC
426733 TGTATCGATACAT
1 TGTATCGATACAT
*
426746 TGTATCGATACAG
1 TGTATCGATACAT
* * *
426759 TGCACCAATACAT
1 TGTATCGATACAT
426772 TGTATCGATACAT
1 TGTATCGATACAT
*
426785 TGTATCGATACAG
1 TGTATCGATACAT
*
426798 TGTACCGATACAT
1 TGTATCGATACAT
*
426811 TGTATCGATACAG
1 TGTATCGATACAT
*
426824 TGTACCGATACA
1 TGTATCGATACA
426836 AAGGGTTTAT
Statistics
Matches: 76, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 76 1.00
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:426787 original size:39 final size:39
Alignment explanation
Indices: 426733--426835 Score: 170
Period size: 39 Copynumber: 2.6 Consensus size: 39
426723 TAGCATTCTC
426733 TGTATCGATACATTGTATCGATACAGTGCACCAATACAT
1 TGTATCGATACATTGTATCGATACAGTGCACCAATACAT
* *
426772 TGTATCGATACATTGTATCGATACAGTGTACCGATACAT
1 TGTATCGATACATTGTATCGATACAGTGCACCAATACAT
* *
426811 TGTATCGATACAGTGTACCGATACA
1 TGTATCGATACATTGTATCGATACA
426836 AAGGGTTTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 60 1.00
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.31
Consensus pattern (39 bp):
TGTATCGATACATTGTATCGATACAGTGCACCAATACAT
Found at i:429295 original size:20 final size:21
Alignment explanation
Indices: 429270--429322 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
429260 ATCGACACAT
*
429270 TGTATCGATACATG-ACCA-AA
1 TGTATCGATACATGCA-AAGAA
*
429290 TGTATCGATACTTGCAAAGAA
1 TGTATCGATACATGCAAAGAA
429311 TGTATCGATACA
1 TGTATCGATACA
429323 GGTGATTGGC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (21 bp):
TGTATCGATACATGCAAAGAA
Found at i:429400 original size:13 final size:13
Alignment explanation
Indices: 429382--429407 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
429372 TACACACAAG
429382 ATGTATCGATACA
1 ATGTATCGATACA
429395 ATGTATCGATACA
1 ATGTATCGATACA
429408 TCCCAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:429425 original size:33 final size:32
Alignment explanation
Indices: 429364--429427 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
429354 CTTAACTGTT
429364 TGTATCGATACACACAAGATGTATCGATACAA
1 TGTATCGATACACACAAGATGTATCGATACAA
*
429396 TGTATCGATACATCCCAA-ATTGTATCGATACA
1 TGTATCGATACA-CACAAGA-TGTATCGATACA
429428 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 13 0.45
33 16 0.55
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACACAAGATGTATCGATACAA
Found at i:431744 original size:62 final size:62
Alignment explanation
Indices: 431449--433978 Score: 2529
Period size: 62 Copynumber: 40.6 Consensus size: 62
431439 CCCTTTTACT
* * * *
431449 CTTTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTC-AAGCCCATATGAGTTGGCGGCAC
1 CTTTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCAC
* * * * * * * * *
431510 CCTTCAGTCTTCAAAAAGTAGGA-TCCTTTTTCCTTTC-AAGCTCACATGAGTTGGTGGCAC
1 CTTTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCAC
* * * **
431570 AC-TTTAATCCTTCAAA-AGTAGGACGCCTTTTTCTTTTCAAA-CCTACACGACATGGTGGCAC
1 -CTTTTAGTCC-TCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCAC
* * * * * * *
431631 C-TTTAGTCCTCAAAGAGTAGGATGCCTTTTTTATTTTTAAAGCCTATACGAGTTGGTGGCAT
1 CTTTTAGTCCTCAAAGAGCAGGACGCC-TTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCAC
* * * * *
431693 CTTTTAGCCCTCAAAGAGCATGACGCATTTTCCTTTTCAAAGCCCACACGAGTGGGTGGCACC
1 CTTTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCA-C
** *
431756 CTTTTAGTCCTCAAAGAGCAGGACATCTTTTTCTTTTCAAA-CCCACACAAGTTGGTGGCATC
1 CTTTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCA-C
* * * *
431818 CTTTT-GTCTTTAAAGAGCATGATGCCTTTTTCCATTTT-AAAGCCCACACGAGTTGGTGGCAC
1 CTTTTAGTCCTCAAAGAGCAGGACGCCTTTTT-C-TTTTCAAAGCCCACACGAGTTGGTGGCAC
* * * *
431880 CCTTTAGTCCTCAAAGAGCAGGACACCTTTTTCTCTTCAAAGCCCACATGAGTTGGTGGCACC
1 CTTTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCA-C
* * * *
431943 CTTTTAGTCCACAAAGAGCAGGACGCCTTTTCCTTTTTAAAGCCCACATGAGTTGGTGGCAC
1 CTTTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCAC
* * * * * * * * *
432005 CTTTTCGTCCCCAAAGAGCAAGAC-ACTTTTTCCTTTTTAAAGCCTACACGAGTAGATGACATC
1 CTTTTAGTCCTCAAAGAGCAGGACGCCTTTTT-CTTTTCAAAGCCCACACGAGTTGGTGGCA-C
** * * * *** *
432068 CTTTTAGTTATTAAAAAGTAGGTTACCTTTTTCTTTTC-AAGCCCACAC-ATGTTGGTTGCATC
1 CTTTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGA-GTTGGTGGCA-C
* * * * *
432130 CTTTT-GTCCTTAAAGAGCAGGATGCCTTTTTCATTTCAAAGCTCACACGAGTTTGTGGCAC
1 CTTTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCAC
* * * *
432191 CATTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTCTTCAAAGCCCACACGAGTTGGTGACACC
1 CTTTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCA-C
* **** * * * *
432254 CTTTTAGCCCTCAAAGAGCAGGGTATCTTTTCCTTTTTAAAGCCCACATGAGTTAGTGGCAC
1 CTTTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCAC
* * *
432316 CTTTTAGTCCTCAAAAAGCAGGATGCCTTTTTCTTTTCAAAGCCCACACGAGTAGGTGGCACC
1 CTTTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCA-C
* * *
432379 CTTTTAGTCCTCAAAGAGCAGGACGCATTTTTCTTTTC-AAGCCCACACGAGTTTGTGGCAT
1 CTTTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCAC
* * * * *
432440 CTTTTTGTCCTCAAAGAGTAGGACACCTTTTTCATTTCAAAGCCCACACGAGTTGGTGGTAC
1 CTTTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCAC
* * ** *
432502 CCTTTAGTCCTCAAAGAGCAGGACGCTTTTTTCTCTTT-AAAGCTTACACAAGTTGGTGGCACC
1 CTTTTAGTCCTCAAAGAGCAGGACGCCTTTTTCT-TTTCAAAGCCCACACGAGTTGGTGGCA-C
* * *
432565 CTTTTAATCCTCAAAGAGTAGGACACC-TTTTCTTTTTCAAAGCCCACACGAGTTGGTGGCACC
1 CTTTTAGTCCTCAAAGAGCAGGACGCCTTTTTC-TTTTCAAAGCCCACACGAGTTGGTGGCA-C
* *
432628 CTTTT-GTCCTCAAAGAGCAGGACG-CATTTTCCTTTCAAAGCCCACACGAGTTGGTGGCAC
1 CTTTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCAC
* * *
432688 CCTTTAGTCCTCAAAGAGCATGACACCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCAC
1 CTTTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCAC
* * * * * * *
432750 CCTTTAGTCCTAAAAGAGTAGGATGCCTTTTTCTTTTC-ATGCCCATACGAGTTAGTGGCAC
1 CTTTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCAC
* * * * * *
432811 C-TTTAGTCCTCAAAGAACAGGACATCTTTTTTCGTTTT-AAATCTCACACGAGTTGGTAGCAC
1 CTTTTAGTCCTCAAAGAGCAGGAC-GCCTTTTTC-TTTTCAAAGCCCACACGAGTTGGTGGCAC
* * * * *
432873 ATTTTAATCCTCAAAGAGCAGGACGCCTTTTCCTTTTCAAAACCCACACGAGTAGGTGGCAC
1 CTTTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCAC
* * *
432935 CTTTTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTC-GAG-CCACACGAGTTGGTGGCTTC
1 C-TTTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGC-AC
* * * *
432997 ATTTT-GTCCTCAAAGAGCAAGATGCCTTTTTCATTTCAAAGCTCACACGCCCTCACGAGTTGGT
1 CTTTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGC-C-CA------CACGAGTTGGT
433061 GGCAC
58 GGCAC
* * *
433066 CCTTTAGTCCTCAAAGAGCATGACACCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCAC
1 CTTTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCAC
* * * * * * *
433128 CCTTTAGTCCTAAAAGAGTAGGATGCCTTTTTCTTTTC-ATGCCCATACGAGTTAGTGGCAC
1 CTTTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCAC
* * * * * *
433189 C-TTTAGTCCTCAAAGAACAGGACATCTTTTTTCGTTTT-AAATCTCACACGAGTTGGTAGCAC
1 CTTTTAGTCCTCAAAGAGCAGGAC-GCCTTTTTC-TTTTCAAAGCCCACACGAGTTGGTGGCAC
* * * * * * *
433251 ATTTTAATCCTCAAAGAGTAGGATGCCTTTTCCTTTTCAAAACCCACACGAGTAGGTGGCAC
1 CTTTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCAC
* * *
433313 CTTTTTAGTCCTCAAAGAGCAGGATGCCTTTTTCTTTTC-GAG-CCACACGAGTTGGTGGCTTC
1 C-TTTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGC-AC
* * * *
433375 ATTTT-GTCCTCAAAGAGCAAGATGCCTTTTTCATTTCAAAGCTCACACGCCCTCACGAGTTGGT
1 CTTTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGC-C-CA------CACGAGTTGGT
433439 GGCAC
58 GGCAC
* * * ** *
433444 CCTTTAGTCTTCAAAGAGTAGGATTCCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACC
1 CTTTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCA-C
* * * * * * *
433507 CTTTTTGTCCTCAAAGAGAAGGATGCCTTTTCCTTTTTAAAGCCCATAGGAGTTGGTGGCAC
1 CTTTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCAC
* * * *
433569 CTTTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACATGAGTAGGTAGCATT
1 CTTTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCA-C
* * **
433632 CTTTTAGTCCTCAAAGGGTAGGACATCTTTTTCTTTTC-AAGCCCACACGAGTTGGTGGCATC
1 CTTTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCA-C
* * * * *
433694 TTTTTA-TCCTCAAAGAGTAGGATGCCTTTTCCTTTTTAAAGCCCACACGAGTTGGTGGCACC
1 CTTTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCA-C
* * * **
433756 CTTTT-GTCCTCAAAGAACAAGATGCCTTTTTCTTTTCAAAGCCCACATAAGTTGGTGGCAC
1 CTTTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCAC
* * * * * *
433817 CCTTTAGTCCTTAAAGAGTAGGATGCCTTTTTCTTTTCAAAGCCTACACGAGTTGGTGACAC
1 CTTTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCAC
* ** * * * *
433879 CCTTTAGTCCTCAAAGAGC-GGAACATCTTTTTCTTTTCAAAGCCTATACAAGTTGGTGACAC
1 CTTTTAGTCCTCAAAGAGCAGG-ACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCAC
* * *
433941 CCTTTAGTCCTCAAATAGAAGGACGCCTTTTTCTTTTC
1 CTTTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTC
433979 TCTTTTGTCC
Statistics
Matches: 2054, Mismatches: 340, Indels: 149
0.81 0.13 0.06
Matches are distributed among these distances:
59 5 0.00
60 163 0.08
61 340 0.17
62 916 0.45
63 514 0.25
64 10 0.00
68 4 0.00
69 10 0.00
70 92 0.04
ACGTcount: A:0.24, C:0.25, G:0.19, T:0.32
Consensus pattern (62 bp):
CTTTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCAC
Found at i:434078 original size:41 final size:39
Alignment explanation
Indices: 434029--434244 Score: 168
Period size: 44 Copynumber: 5.2 Consensus size: 39
434019 TTTTTTTACT
434029 TTTGTCCTCAAAGAGCATGACACACTTGATTTCCTTTTTCC
1 TTTGTCCTCAAAGAGCA-GACACACTT-ATTTCCTTTTTCC
* *
434070 TTTGTCCTCAAAGAGCATGGCGCACCTTATTTCCTTATTTTCTC
1 TTTGTCCTCAAAGAGCA-GACACA-CTTATTTCC-T-TTTTC-C
* * **
434114 TTAGTCCTCAAAGAGCA-AAATGCTT-TTTCCTTTTTTCC
1 TTTGTCCTCAAAGAGCAGACACACTTATTTCC-TTTTTCC
* * *
434152 TTTGTCCTCAAAGAGTAGGACACATTTCATTTCTTTCTTTTCCC
1 TTTGTCCTCAAAGAGCA-GACACACTT-ATTTC---CTTTTTCC
* *
434196 TTTGTCCTCAAAAAGCAGA-ATGCACTATATTTCCTTTCTCC
1 TTTGTCCTCAAAGAGCAGACA--CACT-TATTTCCTTTTTCC
434237 TTTGTCCT
1 TTTGTCCT
434245 TAAAAAGTAG
Statistics
Matches: 141, Mismatches: 20, Indels: 28
0.75 0.11 0.15
Matches are distributed among these distances:
38 16 0.11
39 5 0.04
40 11 0.08
41 45 0.32
42 9 0.06
43 7 0.05
44 46 0.33
45 2 0.01
ACGTcount: A:0.21, C:0.26, G:0.12, T:0.41
Consensus pattern (39 bp):
TTTGTCCTCAAAGAGCAGACACACTTATTTCCTTTTTCC
Done.