Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold887
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: 56202
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35
Found at i:4187 original size:214 final size:214
Alignment explanation
Indices: 3732--4248 Score: 806
Period size: 213 Copynumber: 2.4 Consensus size: 214
3722 TAATACTACT
*
3732 TTGTATTACCTTTTGATAATATATTTATATAATTTACAAAATTTTATGTAAATATAAGATATTTA
1 TTGTATTACCTTTTGATAATATATTTATATAACTTACAAAATTTTATGTAAATATAAGATATTTA
** *
3797 TGTATTAGTACTTTTATTATCTTACATCATTTATGTTTTAAGTAATGTATATGTGTAATTATAAT
66 TGTATTACAACTTTTATTATC-TACATCATTTATGGTTTAAGTAATGTATATGTGTAATTATAAT
*
3862 ATAAATATGTAATAACTTCCATCTATACTTTTGATAATAATTTATCTAATGGATAATATAATTTA
130 ATAAATATGTAATAACTTCCATCTATACTTTTGATAATAATTTATATAATGGATAATATAATTTA
* *
3927 TGTAAATATAATGTTTTAAG
195 CGTAAATATAATATTTTAAG
*
3947 TTGTATTACCTTTTGATAATATATTTACATAA-TTACAAAATTTTATGTAAATATAAGATATTTA
1 TTGTATTACCTTTTGATAATATATTTATATAACTTACAAAATTTTATGTAAATATAAGATATTTA
4011 TGTATTACAACTTTTATTATCTACATCATTTATGGTTTAAGTAATGTATATGTGTAATTATAATA
66 TGTATTACAACTTTTATTATCTACATCATTTATGGTTTAAGTAATGTATATGTGTAATTATAATA
* *
4076 T-AATATGTAATAACTTTCATCTATACTTTTGATAATAATTTTATATCATGGATAATATAATTTA
131 TAAATATGTAATAACTTCCATCTATACTTTTGATAATAA-TTTATATAATGGATAATATAATTTA
*
4140 CGTAAGTATAATATTTTAAG
195 CGTAAATATAATATTTTAAG
* * * ** * *
4160 TTGTATTTCCTTTTCATTAATATATTTATGTAACTTACCATACCTTTTATGTAAATATAATAAAT
1 TTGTATTACCTTTTGA-TAATATATTTATATAACTTA-CA-AAATTTTATGTAAATATAAGATAT
4225 TTATGTATTACAA-TTTTATTATCT
63 TTATGTATTACAACTTTTATTATCT
4249 TTTATCATAA
Statistics
Matches: 279, Mismatches: 18, Indels: 9
0.91 0.06 0.03
Matches are distributed among these distances:
212 36 0.13
213 98 0.35
214 65 0.23
215 34 0.12
216 13 0.05
217 33 0.12
ACGTcount: A:0.37, C:0.07, G:0.08, T:0.48
Consensus pattern (214 bp):
TTGTATTACCTTTTGATAATATATTTATATAACTTACAAAATTTTATGTAAATATAAGATATTTA
TGTATTACAACTTTTATTATCTACATCATTTATGGTTTAAGTAATGTATATGTGTAATTATAATA
TAAATATGTAATAACTTCCATCTATACTTTTGATAATAATTTATATAATGGATAATATAATTTAC
GTAAATATAATATTTTAAG
Found at i:6321 original size:2 final size:2
Alignment explanation
Indices: 6316--6340 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6306 CTTTTTTGTA
6316 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 A
6341 GGTTTGACAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17860 original size:327 final size:328
Alignment explanation
Indices: 17249--18059 Score: 1013
Period size: 327 Copynumber: 2.5 Consensus size: 328
17239 AAATTTCTCT
* ** ** *** * **
17249 TATTT-TCAAATTACGGGGTTTTCTTTTTCGTAAATTTTTTCAAGAGGATTTTCATGGGTTTAAA
1 TATTTCTCAAAATACGTAGTTTTCTACTTCGTAAATTTTTTTGGGAGGATTTTC-TTGGTTTTTA
17313 ATTTTTAAAATTCATCAAATATTATTATTTATTTCATATTAAATCAGTTTTCAAAAATTCATTCA
65 ATTTTTAAAATTCATCAAATATTATTATTTATTTCATATTAAATCAGTTTTCAAAAATTCATTCA
17378 TTTTCATGAGCTTTTTATTTTTTTCTATGAAATTTCCTAGTTTTCGAAATACAGAGTGTTCTACT
130 TTTTCATGAG-TTTTTATTTTTTTCTATGAAATTTCCTA-TTTTCGAAATACAGAGTGTTCTACT
*
17443 CGGTAATTTTTTTCGAGCGGATTTTCTTAGTTTTTAATTTTTAAAATTCATAAAATATTATTATT
193 CGGTAATTTTTTTCGAGCGGATTTTCTTAGTTTTTAATTTTTAAAATTCATAAAATATCATTATT
*
17508 TATTTCATATTAAATCAAGTTTCAAAAATTCATTCATTTTCATGAGTT-TTT-AATTTTTTTCCT
258 TATTTCATATTAAATCAAGTTTCAAAAATTAATTCATTTTCATGAGTTCTTTGAATTTTTTT-CT
17571 T-AA-CC
322 TAAATCC
17576 TATTTCT-AAAATAC-TAAGTTTTCTACTTCGTAAATTTTTTTGGGAGGATTTCTCTTGGTTTTT
1 TATTTCTCAAAATACGT-AGTTTTCTACTTCGTAAATTTTTTTGGGAGGATTT-TCTTGGTTTTT
* * * *
17639 AATTTTTAAAATTTATCAAATATTATTATTTATTTCATAATAAATCAGTCTTGAAAAATTCATTC
64 AATTTTTAAAATTCATCAAATATTATTATTTATTTCATATTAAATCAGTTTTCAAAAATTCATTC
** * *
17704 ATCCTCATGAGTTTTTGATTTTTTTCCT-TGAAATTTCTCT-TTTTCTGAAATAC-GTTGTTTTC
129 ATTTTCATGAGTTTTT-ATTTTTTT-CTATGAAATTTC-CTATTTTC-GAAATACAG-AGTGTTC
* *
17766 TATTTC-GTAATTTTTTTCG-GGGGATTTTTCTT-GATTTTTAATTTTTAAAATTCATAAAATAT
189 TA-CTCGGTAATTTTTTTCGAGCGGA-TTTTCTTAG-TTTTTAATTTTTAAAATTCATAAAATAT
*
17828 CATTATTTATTTCATATTAAATCAATTTTCAAAAATTAATTCATTTTCATGAGTTCTTTGAATTT
251 CATTATTTATTTCATATTAAATCAAGTTTCAAAAATTAATTCATTTTCATGAGTTCTTTGAATTT
17893 TTTTCTTGAAATTCCC
316 TTTTCTT-AAA-T-CC
* * * * *
17909 TTTTTTTCGAAATACGTTGTTTTCTACTTCGT-AATTTCTTTGAGG-GGAGTTTTCTTGGTTTTT
1 TATTTCTCAAAATACGTAGTTTTCTACTTCGTAAATTTTTTTG-GGAGGA-TTTTCTTGGTTTTT
* * * * * *
17972 AATTTTTAAAATTCATAAAATATCATTATTTATTTTATATTAAATTAGTTTTTAAAAATTAATTC
64 AATTTTTAAAATTCATCAAATATTATTATTTATTTCATATTAAATCAGTTTTCAAAAATTCATTC
* *
18037 ATTTTCTTGAGTTTTTAATTTTT
129 ATTTTCATGAGTTTTTATTTTTT
18060 CTTTAAAATT
Statistics
Matches: 420, Mismatches: 42, Indels: 39
0.84 0.08 0.08
Matches are distributed among these distances:
326 16 0.04
327 247 0.59
328 15 0.04
329 9 0.02
330 2 0.00
332 6 0.01
333 99 0.24
334 25 0.06
335 1 0.00
ACGTcount: A:0.29, C:0.11, G:0.09, T:0.52
Consensus pattern (328 bp):
TATTTCTCAAAATACGTAGTTTTCTACTTCGTAAATTTTTTTGGGAGGATTTTCTTGGTTTTTAA
TTTTTAAAATTCATCAAATATTATTATTTATTTCATATTAAATCAGTTTTCAAAAATTCATTCAT
TTTCATGAGTTTTTATTTTTTTCTATGAAATTTCCTATTTTCGAAATACAGAGTGTTCTACTCGG
TAATTTTTTTCGAGCGGATTTTCTTAGTTTTTAATTTTTAAAATTCATAAAATATCATTATTTAT
TTCATATTAAATCAAGTTTCAAAAATTAATTCATTTTCATGAGTTCTTTGAATTTTTTTCTTAAA
TCC
Found at i:17903 original size:167 final size:163
Alignment explanation
Indices: 17186--18059 Score: 952
Period size: 166 Copynumber: 5.3 Consensus size: 163
17176 TTAATCACCA
* * * * * * * *
17186 TAAATTAGTTTTTAAAAATTCTTTTTATTTT-TTGAGTTATTGATTTTCTT-TTGAAATTTCTCT
1 TAAATCAGTTTTCAAAAATTC-ATTCATTTTCATGAGTTTTTAATTTTTTTCTTGAAATTTC-CT
* ** ** * * * * **
17249 TATTT-TCAAATTACGGGGTTTTCTTTTTCGTAAATTTTTTCAAGAGGATTTTCATGGGTTTAAA
64 T-TTTCTGAAA-TACGTAGTTTTCTACTTCGTAATTTTTTTC-GGGGGATTTTC-TTGGTTTTTA
*
17313 ATTTTTAAAATTCATCAAATATTATTATTTATTTCATAT
125 ATTTTTAAAATTCATAAAATATTATTATTTATTTCATAT
17352 TAAATCAGTTTTCAAAAATTCATTCATTTTCATGAGCTTTTT-ATTTTTTTCTATGAAATTTCCT
1 TAAATCAGTTTTCAAAAATTCATTCATTTTCATGAG-TTTTTAATTTTTTTCT-TGAAATTTCCT
* * *
17416 AGTTTTC-GAAATACAG-AGTGTTCTAC-TCGGTAATTTTTTTCGAGCGGATTTTCTTAGTTTTT
64 --TTTTCTGAAATAC-GTAGTTTTCTACTTC-GTAATTTTTTTCG-GGGGATTTTCTTGGTTTTT
17478 AATTTTTAAAATTCATAAAATATTATTATTTATTTCATAT
124 AATTTTTAAAATTCATAAAATATTATTATTTATTTCATAT
17518 TAAATCAAG-TTTCAAAAATTCATTCATTTTCATGAGTTTTTAATTTTTTTCCTT--AA---CCT
1 TAAATC-AGTTTTCAAAAATTCATTCATTTTCATGAGTTTTTAATTTTTTT-CTTGAAATTTCCT
* *
17577 ATTTCTAAAATAC-TAAGTTTTCTACTTCGTAAATTTTTTT-GGGAGGATTTCTCTTGGTTTTTA
64 TTTTCTGAAATACGT-AGTTTTCTACTTCGT-AATTTTTTTCGGG-GGATTT-TCTTGGTTTTTA
* * *
17640 ATTTTTAAAATTTATCAAATATTATTATTTATTTCATAA
125 ATTTTTAAAATTCATAAAATATTATTATTTATTTCATAT
* * ** *
17679 TAAATCAGTCTTGAAAAATTCATTCATCCTCATGAGTTTTTGATTTTTTTCCTTGAAATTTCTCT
1 TAAATCAGTTTTCAAAAATTCATTCATTTTCATGAGTTTTTAATTTTTTT-CTTGAAATTTC-CT
* * *
17744 TTTTCTGAAATACGTTGTTTTCTATTTCGTAATTTTTTTCGGGGGATTTTTCTTGATTTTTAATT
64 TTTTCTGAAATACGTAGTTTTCTACTTCGTAATTTTTTTCGGGGGA-TTTTCTTGGTTTTTAATT
*
17809 TTTAAAATTCATAAAATATCATTATTTATTTCATAT
128 TTTAAAATTCATAAAATATTATTATTTATTTCATAT
* * *
17845 TAAATCAATTTTCAAAAATTAATTCATTTTCATGAGTTCTTTGAATTTTTTTCTTGAAATTCCCT
1 TAAATCAGTTTTCAAAAATTCATTCATTTTCATGAGTT-TTT-AATTTTTTTCTTGAAATTTCCT
* * *
17910 TTTTTTCGAAATACGTTGTTTTCTACTTCGTAATTTCTTT-GAGGGGAGTTTTCTTGGTTTTTAA
64 TTTTCT-GAAATACGTAGTTTTCTACTTCGTAATTTTTTTCG-GGGGA-TTTTCTTGGTTTTTAA
* *
17974 TTTTTAAAATTCATAAAATATCATTATTTATTTTATAT
126 TTTTTAAAATTCATAAAATATTATTATTTATTTCATAT
* * * *
18012 TAAATTAGTTTTTAAAAATTAATTCATTTTCTTGAGTTTTTAATTTTT
1 TAAATCAGTTTTCAAAAATTCATTCATTTTCATGAGTTTTTAATTTTT
18060 CTTTAAAATT
Statistics
Matches: 614, Mismatches: 60, Indels: 69
0.83 0.08 0.09
Matches are distributed among these distances:
159 5 0.01
160 26 0.04
161 107 0.17
163 2 0.00
164 2 0.00
165 19 0.03
166 220 0.36
167 207 0.34
168 25 0.04
169 1 0.00
ACGTcount: A:0.28, C:0.10, G:0.09, T:0.52
Consensus pattern (163 bp):
TAAATCAGTTTTCAAAAATTCATTCATTTTCATGAGTTTTTAATTTTTTTCTTGAAATTTCCTTT
TTCTGAAATACGTAGTTTTCTACTTCGTAATTTTTTTCGGGGGATTTTCTTGGTTTTTAATTTTT
AAAATTCATAAAATATTATTATTTATTTCATAT
Found at i:19910 original size:167 final size:166
Alignment explanation
Indices: 19480--19923 Score: 513
Period size: 167 Copynumber: 2.7 Consensus size: 166
19470 GTGGTAAAAT
* *
19480 TAAATATTAATCATTTTTCAATCTTTTATATTCCTATTGGGGTCCGTAGGGGTATAAAAGATTTC
1 TAAATATTAATCATTTTTTAATCTTTTATATTCCTATGGGGGTCCGTA-GGGTATAAAAGATTTC
* * ** * *
19545 AAAAGCTTTTCGTATCTTTTTGGGCTTCCATTAAGGTATGAAATGGTATTTTCCAAAAATGAATA
65 AAAAACTTTTCGTATCTTTTCGGAATTCCATTAAGGTACGAAATGGTATTTTCCAAAAATCAATA
* **
19610 AATAAATTGAATTAAATAAACACTTTCATAATTGAAA
130 AATAAATTAAATTAAATAAACACTTTCATAATCCAAA
* *
19647 TAAATATTAATCATTTTTTAATCTTTTATATTCCTATGGGGGTTCGTAAAGGTATAAAAGATTTC
1 TAAATATTAATCATTTTTTAATCTTTTATATTCCTATGGGGGTCCGT-AGGGTATAAAAGATTTC
** * * * *
19712 AAAAAAATTTCGTATCTTTTC--AAGCTTCCATTAAGGAACGAAATGGTATTTTTCGACAA-CAA
65 AAAAACTTTTCGTATCTTTTCGGAA--TTCCATTAAGGTACGAAATGGTATTTTCCAAAAATCAA
* * * * *
19774 -ATA-AAATTAAATTAAATCATCATTTTTATAA-CCAAGA
128 TAAATAAATTAAATTAAATAAACACTTTCATAATCCAA-A
* *
19811 TAAATTTTAAATCTTTCCTTTTAAATCTTTTATATTCCTATGGGGGTCCGTAGGGTATAAAAGAT
1 TAAATATT-AATCATT--TTTT-AATCTTTTATATTCCTATGGGGGTCCGTAGGGTATAAAAGAT
* *
19876 TTCAAAAACTTTTCGCATCTTTTCGGAATTCCATTAAGGTACCAAATG
62 TTCAAAAACTTTTCGTATCTTTTCGGAATTCCATTAAGGTACGAAATG
19924 AATTTTTGTA
Statistics
Matches: 234, Mismatches: 33, Indels: 20
0.82 0.11 0.07
Matches are distributed among these distances:
163 2 0.01
164 31 0.13
165 8 0.03
166 2 0.01
167 161 0.69
168 28 0.12
169 2 0.01
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.39
Consensus pattern (166 bp):
TAAATATTAATCATTTTTTAATCTTTTATATTCCTATGGGGGTCCGTAGGGTATAAAAGATTTCA
AAAACTTTTCGTATCTTTTCGGAATTCCATTAAGGTACGAAATGGTATTTTCCAAAAATCAATAA
ATAAATTAAATTAAATAAACACTTTCATAATCCAAA
Found at i:20566 original size:156 final size:154
Alignment explanation
Indices: 20405--20705 Score: 370
Period size: 155 Copynumber: 1.9 Consensus size: 154
20395 TAGAACCAAA
* ** *
20405 TCCTAGGTTGTCATCGGGTCTGCTTTAATACCGATGATGGGTATTTAGGATAGGTTCATCCCATT
1 TCCTAGGTTGTCACCGAATCTGCTTTAATACCGAAGATGGGTATTTAGGATAGGTTCATCCCA-T
* * * * *
20470 TTGTAATTTTTTTTAAGTCCTTTAGGGATATCTGGCACTTCTACGTCGAAGATAT-CCTCTAGGG
65 CTATAATCTTTTTTAAGTCCTTTAGGGATATCAGGCACTTCTACGTCGAAGATATCCCT-TAAGG
*
20534 GTATTTTGGTAATTTTTTAGATCTGAG
129 GTATTTTCGT-ATTTTTTAGATCTGAG
** * * * ** *
20561 TCCTAGGTTGTCACCGAATCTGCTTTTTTGCTGAAGGTGGGTATTTAGGATAGGTTTGTCTCATC
1 TCCTAGGTTGTCACCGAATCTGCTTTAATACCGAAGATGGGTATTTAGGATAGGTTCATCCCATC
* * * *
20626 TATAATCTTTTTTAAGTCCTTTAGGGGTATCAGGTACTTTTACGTCGAAGTTATCCCTTAAGGGT
66 TATAATCTTTTTTAAGTCCTTTAGGGATATCAGGCACTTCTACGTCGAAGATATCCCTTAAGGGT
20691 ATTTTCGTATTTTTT
131 ATTTTCGTATTTTTT
20706 CTTGAACTTA
Statistics
Matches: 122, Mismatches: 22, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
154 7 0.06
155 61 0.50
156 54 0.44
ACGTcount: A:0.20, C:0.15, G:0.22, T:0.43
Consensus pattern (154 bp):
TCCTAGGTTGTCACCGAATCTGCTTTAATACCGAAGATGGGTATTTAGGATAGGTTCATCCCATC
TATAATCTTTTTTAAGTCCTTTAGGGATATCAGGCACTTCTACGTCGAAGATATCCCTTAAGGGT
ATTTTCGTATTTTTTAGATCTGAG
Found at i:30360 original size:26 final size:26
Alignment explanation
Indices: 30321--30373 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
30311 GGTAATAGCC
*
30321 AGTTCTTAACTGTTGTTACAAATTCT
1 AGTTCTTAACTGTTATTACAAATTCT
*
30347 AGTTCTTAATTGTTATTACAAATTCT
1 AGTTCTTAACTGTTATTACAAATTCT
30373 A
1 A
30374 ACATTTCTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.30, C:0.13, G:0.09, T:0.47
Consensus pattern (26 bp):
AGTTCTTAACTGTTATTACAAATTCT
Found at i:34390 original size:15 final size:16
Alignment explanation
Indices: 34365--34401 Score: 67
Period size: 15 Copynumber: 2.4 Consensus size: 16
34355 TAGATAGTCT
34365 AATGAGAAGTAGCATA
1 AATGAGAAGTAGCATA
34381 AATG-GAAGTAGCATA
1 AATGAGAAGTAGCATA
34396 AATGAG
1 AATGAG
34402 GTCAAAAGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 15 0.75
16 5 0.25
ACGTcount: A:0.49, C:0.05, G:0.27, T:0.19
Consensus pattern (16 bp):
AATGAGAAGTAGCATA
Found at i:37729 original size:163 final size:161
Alignment explanation
Indices: 37397--37805 Score: 579
Period size: 163 Copynumber: 2.5 Consensus size: 161
37387 AAAATTCTTT
* * ** * * * *
37397 AAATATTATCATTTAATTTCCATTTAATTAGTTTTAAAAAATTTATTCATTTTCATTCA-TTTTT
1 AAATATTATTATTTATTTTATATTAAATTAGTTTTCAAAAATTAATTCATTTTCA-TGAGTTTTT
* *
37461 CATTTTTTTCTTGAAATTTTCCTACTTTCGAAATACAGAGTTTTCTACTTCGTAATTTTTTTGGG
65 CATTTTTTTCTTGAAA--TTCC-ACTTTCGAAATACAGAGTTTTCTACTCCGTAATTTTTTCGGG
37526 GGATTTTTCTTGGTTTTTAATTTTTAAAATTTAAC
127 GGATTTTTCTTGGTTTTTAATTTTTAAAATTTAAC
37561 AAATATTATTATTTATTTTATATTAAATTAGTTTTCAAAAATTAATTCATTTTCATGAGTTTTTT
1 AAATATTATTATTTATTTTATATTAAATTAGTTTTCAAAAATTAATTCATTTTCATGAG-TTTTT
*
37626 CATTTTTTTCTTGAAATTCC-CTTTCGAAATACAGAGTTTTTTACTCCGTAAATTTTTTCGGGGA
65 CATTTTTTTCTTGAAATTCCACTTTCGAAATACAGAGTTTTCTACTCCGT-AATTTTTTCGGGG-
* *
37690 GATTTTTTTTGGTTTTTAATTTTTAAAATTTATC
128 GATTTTTCTTGGTTTTTAATTTTTAAAATTTAAC
* * * * *
37724 AAATATTATTATTTATTTCATATTAAATTATTTTTCAAAAATTCACTCATTTTCTTGAGTTTTTC
1 AAATATTATTATTTATTTTATATTAAATTAGTTTTCAAAAATTAATTCATTTTCATGAGTTTTTC
37789 ATTTTTTTCTTGAAATT
66 ATTTTTTTCTTGAAATT
37806 TTCTTATTTT
Statistics
Matches: 223, Mismatches: 18, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
161 27 0.12
162 35 0.16
163 92 0.41
164 48 0.22
165 21 0.09
ACGTcount: A:0.28, C:0.10, G:0.08, T:0.54
Consensus pattern (161 bp):
AAATATTATTATTTATTTTATATTAAATTAGTTTTCAAAAATTAATTCATTTTCATGAGTTTTTC
ATTTTTTTCTTGAAATTCCACTTTCGAAATACAGAGTTTTCTACTCCGTAATTTTTTCGGGGGAT
TTTTCTTGGTTTTTAATTTTTAAAATTTAAC
Found at i:37917 original size:166 final size:163
Alignment explanation
Indices: 37385--37923 Score: 419
Period size: 163 Copynumber: 3.3 Consensus size: 163
37375 GTTTCGAACA
* * * * * * * *
37385 TTAAAATTCTTTAAATATTATCATTTAATTTC-CATTTAATTAGTTTTAAAAAATTTATTCATTT
1 TTAAAATTCATCAAATATTATCATTGAA-CTCACATTAAATTAGTTTTCAAAAATTAACTCATTT
* * *
37449 TCATTCA--TTTTTCATTTTTTTCTTGAAATTTTCCTACTTTCGAAATACAGAGTTTTCTACTTC
65 TCA-TGAGTTTTTTCATTTTTTTCTTGAAA--TTCC-A-TTTCGAAATAAAGAGTTTTCTACTCC
** * *** **
37512 GT-AAT-TTTTTTGGGGGATTTTTCTTGGTTTTTAATTT
125 GTAAATATTTTCAGGGAGATTTTTCTCAATTTAAAATTT
* * * * ** * * *
37549 TTAAAATTTAACAAATATTATTATTTATTTTATATTAAATTAGTTTTCAAAAATTAATTCATTTT
1 TTAAAATTCATCAAATATTATCATTGAACTCACATTAAATTAGTTTTCAAAAATTAACTCATTTT
* * *
37614 CATGAGTTTTTTCATTTTTTTCTTGAAATTCCCTTTCGAAATACAGAGTTTTTTACTCCGTAAAT
66 CATGAGTTTTTTCATTTTTTTCTTGAAATTCCATTTCGAAATAAAGAGTTTTCTACTCCGTAAAT
* * * *** **
37679 TTTTTCGGGGAGATTTTTTTTGGTTTTTAATTT
131 ATTTTCAGGGAGATTTTTCTCAATTTAAAATTT
* * * ** * * *
37712 TTAAAATTTATCAAATATTATTATTTATTTCATATTAAATTATTTTTCAAAAATTCACTCATTTT
1 TTAAAATTCATCAAATATTATCATTGAACTCACATTAAATTAGTTTTCAAAAATTAACTCATTTT
* * **
37777 CTTGAG-TTTTTCATTTTTTTCTTGAAATTTTCTTATTTTTAAA-AAATTGAGTTTTCTACTCCG
66 CATGAGTTTTTTCATTTTTTTCTTGAAA--TTC-CATTTCGAAATAAA--GAGTTTTCTACTCCG
37840 TAAATATTTTCAGGGAGATTTTTCTCAATTTAAAATTT
126 TAAATATTTTCAGGGAGATTTTTCTCAATTTAAAATTT
** * *
37878 TTAAAATTCATTTTAATATTGTCATTGAACTC-CATTAAATCAGTTT
1 TTAAAATTCA-TCAAATATTATCATTGAACTCACATTAAATTAGTTT
37924 GAGAAATTCA
Statistics
Matches: 314, Mismatches: 50, Indels: 20
0.82 0.13 0.05
Matches are distributed among these distances:
161 26 0.08
162 24 0.08
163 101 0.32
164 58 0.18
165 27 0.09
166 64 0.20
167 14 0.04
ACGTcount: A:0.29, C:0.10, G:0.08, T:0.53
Consensus pattern (163 bp):
TTAAAATTCATCAAATATTATCATTGAACTCACATTAAATTAGTTTTCAAAAATTAACTCATTTT
CATGAGTTTTTTCATTTTTTTCTTGAAATTCCATTTCGAAATAAAGAGTTTTCTACTCCGTAAAT
ATTTTCAGGGAGATTTTTCTCAATTTAAAATTT
Found at i:38338 original size:17 final size:16
Alignment explanation
Indices: 38313--38344 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
38303 TGGAAAATGG
38313 AAAAAGAAAAAATAAT
1 AAAAAGAAAAAATAAT
38329 AAAAATGAAAAAATAA
1 AAAAA-GAAAAAATAA
38345 ATGGGCCATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.81, C:0.00, G:0.06, T:0.12
Consensus pattern (16 bp):
AAAAAGAAAAAATAAT
Found at i:39708 original size:30 final size:30
Alignment explanation
Indices: 39672--39734 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
39662 TATTTTAGAG
39672 AAAGGAATAAAATTAAACATAACAATAAAT
1 AAAGGAATAAAATTAAACATAACAATAAAT
*
39702 AAAGGAATAAAATTAAACATAATAATAAAT
1 AAAGGAATAAAATTAAACATAACAATAAAT
39732 AAA
1 AAA
39735 TCTTATTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.68, C:0.05, G:0.06, T:0.21
Consensus pattern (30 bp):
AAAGGAATAAAATTAAACATAACAATAAAT
Found at i:39917 original size:3 final size:3
Alignment explanation
Indices: 39911--39936 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
39901 CTATCCTAAA
39911 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
39937 AGATTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:45290 original size:16 final size:16
Alignment explanation
Indices: 45269--45301 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
45259 ATGAACTTAA
45269 AACAAAATGGACAATG
1 AACAAAATGGACAATG
45285 AACAAAATGGACAATG
1 AACAAAATGGACAATG
45301 A
1 A
45302 TCAATGACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.12, G:0.18, T:0.12
Consensus pattern (16 bp):
AACAAAATGGACAATG
Found at i:45720 original size:30 final size:32
Alignment explanation
Indices: 45668--45732 Score: 89
Period size: 30 Copynumber: 2.1 Consensus size: 32
45658 CTTAAATAAA
* *
45668 TTAATAAGATGTTTATATCAATTATGATAACC
1 TTAATAAGATGTTTACATCAATTATAATAACC
*
45700 TTAATAA-ATG-TTACATCAATTATAATAATC
1 TTAATAAGATGTTTACATCAATTATAATAACC
45730 TTA
1 TTA
45733 TAACCAAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
30 20 0.67
31 3 0.10
32 7 0.23
ACGTcount: A:0.43, C:0.09, G:0.06, T:0.42
Consensus pattern (32 bp):
TTAATAAGATGTTTACATCAATTATAATAACC
Done.