Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1421
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: 311925
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 2 of 2
Found at i:205760 original size:30 final size:30
Alignment explanation
Indices: 205726--205822 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
205716 TAAACTAAAA
*
205726 TGAGCTAAGTTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * * *
205756 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
205786 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
205815 ATGAGCTA
1 -TGAGCTA
205823 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:208014 original size:12 final size:12
Alignment explanation
Indices: 207999--208029 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
207989 TTCTTTTTGC
207999 TTTTCAAAGGCT
1 TTTTCAAAGGCT
208011 TTTTCAAAGGCT
1 TTTTCAAAGGCT
208023 TTTTCAA
1 TTTTCAA
208030 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:208106 original size:6 final size:6
Alignment explanation
Indices: 208090--208139 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
208080 TTTCTTTTTA
*
208090 TTTCAT TTTCTT TTTCTT CTCTTGCTT TTTCTT TTTC-T TTTC-T TTTCTT
1 TTTCTT TTTCTT TTTCTT -T-TT-CTT TTTCTT TTTCTT TTTCTT TTTCTT
208139 T
1 T
208140 GTTTTCTCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
5 10 0.26
6 20 0.51
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (6 bp):
TTTCTT
Found at i:208122 original size:37 final size:37
Alignment explanation
Indices: 208079--208149 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
208069 CTTGCCTCTC
208079 TTTTCTTTTT-ATTTCATTTTCTTT-TTCTTCTCTTGCT
1 TTTTCTTTTTCATTTC-TTTTCTTTGTT-TTCTCTTGCT
*
208116 TTTTCTTTTTCTTTTCTTTTCTTTGTTTTCTCTT
1 TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTT
208150 TACAAGAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 25 0.81
38 6 0.19
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (37 bp):
TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTTGCT
Found at i:208150 original size:16 final size:16
Alignment explanation
Indices: 208075--208135 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
208065 GCCTCTTGCC
*
208075 TCTCTTTTCTTTTTAT
1 TCTCTTTTCTTTTTCT
208091 T-TCATTTTCTTTTTCT
1 TCTC-TTTTCTTTTTCT
*
208107 TCTC-TTGCTTTTTCTT
1 TCTCTTTTCTTTTTC-T
*
208123 TTTCTTTTCTTTT
1 TCTCTTTTCTTTT
208136 CTTTGTTTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
15 11 0.30
16 17 0.46
17 9 0.24
ACGTcount: A:0.03, C:0.20, G:0.02, T:0.75
Consensus pattern (16 bp):
TCTCTTTTCTTTTTCT
Found at i:210096 original size:30 final size:30
Alignment explanation
Indices: 210062--210158 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
210052 TAAACTAAAA
*
210062 TGAGCTAAGTTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * * *
210092 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
210122 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
210151 ATGAGCTA
1 -TGAGCTA
210159 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:212367 original size:22 final size:21
Alignment explanation
Indices: 212336--212386 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
212326 ACCTCTTTGA
*
212336 ACCATTACCAATTCGTACCAAAT
1 ACCA-TACCAATTCCTACC-AAT
*
212359 ACCATACCATTTCCTACCAAT
1 ACCATACCAATTCCTACCAAT
*
212380 TCCATAC
1 ACCATAC
212387 TATTTCGAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 9 0.36
22 12 0.48
23 4 0.16
ACGTcount: A:0.35, C:0.35, G:0.02, T:0.27
Consensus pattern (21 bp):
ACCATACCAATTCCTACCAAT
Found at i:212386 original size:21 final size:21
Alignment explanation
Indices: 212341--212403 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
212331 TTTGAACCAT
* *
212341 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
212363 TACCATTTCCTACCAATTCCA
1 TACCATTTCGTACCAATTCCA
* *
212384 TACTATTTCGAACCAATTCC
1 TACCATTTCGTACCAATTCC
212404 CAAATACCAA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
21 23 0.66
22 12 0.34
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:213042 original size:30 final size:30
Alignment explanation
Indices: 213008--213104 Score: 88
Period size: 30 Copynumber: 3.2 Consensus size: 30
212998 TAAACTAAAA
* *
213008 TGAGCTAAGCTTTAGCTTGTGAGCTAAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
* * * * *
213038 TGAGCTGAGATTAAACTCCTAAGCTAAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
* * *
213068 TAAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGATTTAGCTCGTGAGCT-AAAGT
213098 TGAGCTA
1 TGAGCTA
213105 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 16, Indels: 2
0.74 0.24 0.03
Matches are distributed among these distances:
30 46 0.92
31 4 0.08
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.30
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
Found at i:219466 original size:20 final size:20
Alignment explanation
Indices: 219420--219466 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
219410 AGCTCGTTTC
*
219420 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
219440 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
219460 CAGCTCA
1 CAGCTCA
219467 ATTTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:234703 original size:68 final size:67
Alignment explanation
Indices: 234631--234778 Score: 167
Period size: 67 Copynumber: 2.2 Consensus size: 67
234621 TCATGTGTAT
* * * *
234631 AAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCAT
1 AAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCAT
234693 GTAGAC
62 GTAGAC
** * *
234699 AAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAG
1 AAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGTAG
234764 AC
66 AC
234766 AAGAGAGCTACGA
1 AAGAGAGCTACGA
234779 GATAAACTGG
Statistics
Matches: 68, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
64 20 0.29
65 7 0.10
66 4 0.06
67 26 0.38
68 11 0.16
ACGTcount: A:0.32, C:0.17, G:0.29, T:0.22
Consensus pattern (67 bp):
AAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGTAG
AC
Found at i:234733 original size:64 final size:64
Alignment explanation
Indices: 234653--234836 Score: 194
Period size: 67 Copynumber: 2.8 Consensus size: 64
234643 AGACATTATG
* *
234653 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
234717 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
234782 AA
63 AA
* * * *
234784 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
234837 CGAACTATAT
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 21 0.21
65 8 0.08
66 16 0.16
67 31 0.32
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:235793 original size:25 final size:23
Alignment explanation
Indices: 235739--235794 Score: 67
Period size: 25 Copynumber: 2.3 Consensus size: 23
235729 TTGTTGAGAG
235739 CAGAATTTTCTTTGAGTTTTCTC
1 CAGAATTTTCTTTGAGTTTTCTC
* *
235762 CAAAATTTCTCTCTTGAGTTTTCTT
1 CAGAATTT-TCT-TTGAGTTTTCTC
*
235787 TAGAATTT
1 CAGAATTT
235795 GTTTTAACAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 7 0.26
24 3 0.11
25 17 0.63
ACGTcount: A:0.21, C:0.16, G:0.11, T:0.52
Consensus pattern (23 bp):
CAGAATTTTCTTTGAGTTTTCTC
Found at i:242279 original size:30 final size:30
Alignment explanation
Indices: 242194--242281 Score: 90
Period size: 30 Copynumber: 2.9 Consensus size: 30
242184 TAAGCTAAAA
* *
242194 TGAGCTAAGCTTTAGC-CCTTAAGCTAAAGT
1 TGAGCTAAGATTTAGCTCC-TAAGCTGAAGT
*
242224 TGAGCTGAGATTATA-CTCCTAAGCTGAAGT
1 TGAGCTAAGATT-TAGCTCCTAAGCTGAAGT
* * *
242254 TGAGCTAAGGTTTAGCTCGTGAGCTGAA
1 TGAGCTAAGATTTAGCTCCTAAGCTGAA
242282 TATAAGCTAG
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
29 2 0.04
30 42 0.88
31 4 0.08
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCCTAAGCTGAAGT
Found at i:248351 original size:13 final size:13
Alignment explanation
Indices: 248333--248369 Score: 58
Period size: 12 Copynumber: 2.9 Consensus size: 13
248323 TCAAGTAAGT
248333 TTCAAAAAAAAAA
1 TTCAAAAAAAAAA
248346 TTC-AAAAAAAAA
1 TTCAAAAAAAAAA
*
248358 TTGAAAAAAAAA
1 TTCAAAAAAAAA
248370 CAAAATCTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.76, C:0.05, G:0.03, T:0.16
Consensus pattern (13 bp):
TTCAAAAAAAAAA
Found at i:248369 original size:17 final size:18
Alignment explanation
Indices: 248349--248382 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
248339 AAAAAAATTC
248349 AAAAAAAAAT-TGAAAAA
1 AAAAAAAAATCTGAAAAA
*
248366 AAAACAAAATCTGAAAA
1 AAAAAAAAATCTGAAAA
248383 TTTGGACATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.76, C:0.06, G:0.06, T:0.12
Consensus pattern (18 bp):
AAAAAAAAATCTGAAAAA
Found at i:248380 original size:18 final size:16
Alignment explanation
Indices: 248349--248382 Score: 50
Period size: 18 Copynumber: 2.0 Consensus size: 16
248339 AAAAAAATTC
248349 AAAAAAAAATTGAAAA
1 AAAAAAAAATTGAAAA
248365 AAAAACAAAATCTGAAAA
1 AAAAA-AAAAT-TGAAAA
248383 TTTGGACATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 5 0.31
18 6 0.38
ACGTcount: A:0.76, C:0.06, G:0.06, T:0.12
Consensus pattern (16 bp):
AAAAAAAAATTGAAAA
Found at i:249448 original size:30 final size:28
Alignment explanation
Indices: 249412--249467 Score: 76
Period size: 30 Copynumber: 1.9 Consensus size: 28
249402 AAGCGAAAAA
* *
249412 GAAAAAGAGTGTGTGCAAGAAAGTAAAGTT
1 GAAAAAGAGAGTGAGCAA-AAAG-AAAGTT
249442 GAAAAAGAGAGTGAGCAAAAAGAAAG
1 GAAAAAGAGAGTGAGCAAAAAGAAAG
249468 CGTGGAAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 4 0.17
29 4 0.17
30 16 0.67
ACGTcount: A:0.54, C:0.04, G:0.30, T:0.12
Consensus pattern (28 bp):
GAAAAAGAGAGTGAGCAAAAAGAAAGTT
Found at i:253806 original size:14 final size:14
Alignment explanation
Indices: 253764--253808 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
253754 TTAAAGAAGC
253764 AACTCATTAAATTA
1 AACTCATTAAATTA
* *
253778 AATTCATCAAA-TA
1 AACTCATTAAATTA
*
253791 AACTCATTTAATTA
1 AACTCATTAAATTA
253805 AACT
1 AACT
253809 AAGATGAGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.36
Consensus pattern (14 bp):
AACTCATTAAATTA
Found at i:254307 original size:29 final size:29
Alignment explanation
Indices: 254274--254362 Score: 160
Period size: 29 Copynumber: 3.1 Consensus size: 29
254264 ATAACCAAAC
* *
254274 CTACAAAAACTTTATATCCATAAACCCAT
1 CTACATAAACTTCATATCCATAAACCCAT
254303 CTACATAAACTTCATATCCATAAACCCAT
1 CTACATAAACTTCATATCCATAAACCCAT
254332 CTACATAAACTTCATATCCATAAACCCAT
1 CTACATAAACTTCATATCCATAAACCCAT
254361 CT
1 CT
254363 TTGAATCCTT
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 58 1.00
ACGTcount: A:0.42, C:0.30, G:0.00, T:0.28
Consensus pattern (29 bp):
CTACATAAACTTCATATCCATAAACCCAT
Found at i:254311 original size:14 final size:14
Alignment explanation
Indices: 254292--254362 Score: 70
Period size: 14 Copynumber: 4.9 Consensus size: 14
254282 ACTTTATATC
254292 CATAAACCCATCTA
1 CATAAACCCATCTA
* * *
254306 CATAAACTTCATATC
1 CATAAAC-CCATCTA
254321 CATAAACCCATCTA
1 CATAAACCCATCTA
* * *
254335 CATAAACTTCATATC
1 CATAAAC-CCATCTA
254350 CATAAACCCATCT
1 CATAAACCCATCT
254363 TTGAATCCTT
Statistics
Matches: 44, Mismatches: 11, Indels: 4
0.75 0.19 0.07
Matches are distributed among these distances:
14 22 0.50
15 22 0.50
ACGTcount: A:0.41, C:0.32, G:0.00, T:0.27
Consensus pattern (14 bp):
CATAAACCCATCTA
Found at i:254326 original size:15 final size:15
Alignment explanation
Indices: 254280--254356 Score: 77
Period size: 15 Copynumber: 5.3 Consensus size: 15
254270 AAACCTACAA
*
254280 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* * *
254295 AAAC-CCATCTACAT
1 AAACTTCATATCCAT
254309 AAACTTCATATCCAT
1 AAACTTCATATCCAT
* * *
254324 AAAC-CCATCTACAT
1 AAACTTCATATCCAT
254338 AAACTTCATATCCAT
1 AAACTTCATATCCAT
254353 AAAC
1 AAAC
254357 CCATCTTTGA
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
14 21 0.45
15 26 0.55
ACGTcount: A:0.43, C:0.29, G:0.00, T:0.29
Consensus pattern (15 bp):
AAACTTCATATCCAT
Found at i:254943 original size:19 final size:19
Alignment explanation
Indices: 254919--254962 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
254909 TAAACTAAAA
254919 TGAGCTAAGCTTTAGCTCG
1 TGAGCTAAGCTTTAGCTCG
*
254938 TGAGCTAAGGTTTAGCTCG
1 TGAGCTAAGCTTTAGCTCG
254957 TGAGCT
1 TGAGCT
254963 GAATATGAGC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.20, C:0.18, G:0.30, T:0.32
Consensus pattern (19 bp):
TGAGCTAAGCTTTAGCTCG
Found at i:257121 original size:30 final size:30
Alignment explanation
Indices: 257051--257132 Score: 87
Period size: 30 Copynumber: 2.7 Consensus size: 30
257041 TTTTGTTTCA
* *
257051 ATTTCTTTTTCATCTTCTTTTTCACTCTCAG
1 ATTTCTTTTTCTTC-TCTTTTTCAATCTCAG
257082 ATTTC-TTTTCGTTCTCTTTTTCAATCTCA-
1 ATTTCTTTTTC-TTCTCTTTTTCAATCTCAG
* *
257111 TTTTCTTTTTCTTTTTCTTTTT
1 ATTTCTTTTTC-TTCTCTTTTT
257133 TCTTTTCAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
29 4 0.09
30 33 0.75
31 7 0.16
ACGTcount: A:0.10, C:0.22, G:0.02, T:0.66
Consensus pattern (30 bp):
ATTTCTTTTTCTTCTCTTTTTCAATCTCAG
Found at i:257210 original size:5 final size:5
Alignment explanation
Indices: 257200--257256 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
257190 CTCTTGCCTC
*
257200 TCTTT TCTTT T-TATT TCGTTT TCTTT T-TCT TCTTT CTCTTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TCTTT -TC-TTT TCTTT
257247 TCTTT TCTTT
1 TCTTT TCTTT
257257 GTTTTCTCTT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
4 4 0.09
5 28 0.64
6 8 0.18
7 4 0.09
ACGTcount: A:0.02, C:0.19, G:0.02, T:0.77
Consensus pattern (5 bp):
TCTTT
Found at i:257239 original size:15 final size:14
Alignment explanation
Indices: 257200--257256 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
257190 CTCTTGCCTC
*
257200 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-CT
257215 TCGTTTTCTTTTTCT
1 TC-TTTTCTTTTTCT
257230 TCTTTCTCTTTTTCTTT
1 TCTTT-TCTTTTTC--T
257247 TCTTTTCTTT
1 TCTTTTCTTT
257257 GTTTTCTCTT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
14 3 0.08
15 13 0.35
16 15 0.41
17 6 0.16
ACGTcount: A:0.02, C:0.19, G:0.02, T:0.77
Consensus pattern (14 bp):
TCTTTTCTTTTTCT
Found at i:259400 original size:17 final size:17
Alignment explanation
Indices: 259375--259417 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
259365 GAGACAGCCA
*
259375 CCATACATGCACTTAAG
1 CCATTCATGCACTTAAG
* * *
259392 CCATTCATGCATTTGAT
1 CCATTCATGCACTTAAG
259409 CCATTCATG
1 CCATTCATG
259418 GACTAGCCTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.28, C:0.28, G:0.12, T:0.33
Consensus pattern (17 bp):
CCATTCATGCACTTAAG
Found at i:259899 original size:30 final size:30
Alignment explanation
Indices: 259814--259910 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
259804 TAAACTAAAA
* *
259814 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
* * * * * *
259844 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
259874 TGAGCTAAGGTTTAGCTCGTGAGCTGAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
259903 ATGAGCTA
1 -TGAGCTA
259911 GGAGTGAGCT
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 1 0.02
30 51 0.98
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
Found at i:260966 original size:19 final size:19
Alignment explanation
Indices: 260942--260979 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
260932 ATAACTAAAC
260942 AATTTA-ACAGCAATAATTA
1 AATTTAGACA-CAATAATTA
*
260961 AATTTAGACATAATAATTA
1 AATTTAGACACAATAATTA
260980 TAAGTCAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.53, C:0.08, G:0.05, T:0.34
Consensus pattern (19 bp):
AATTTAGACACAATAATTA
Found at i:262098 original size:20 final size:20
Alignment explanation
Indices: 262073--262111 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
262063 ATGGATATTT
262073 TGCATAGAAATTCAAAGATC
1 TGCATAGAAATTCAAAGATC
262093 TGCATAGAAATTCAAAGAT
1 TGCATAGAAATTCAAAGAT
262112 TTCTCTTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.46, C:0.13, G:0.15, T:0.26
Consensus pattern (20 bp):
TGCATAGAAATTCAAAGATC
Found at i:262859 original size:12 final size:12
Alignment explanation
Indices: 262842--262898 Score: 51
Period size: 12 Copynumber: 4.8 Consensus size: 12
262832 CTCTCTCAAA
262842 CTCTTTTTCATT
1 CTCTTTTTCATT
*
262854 CTCTTTTTCAAT
1 CTCTTTTTCATT
* *
262866 CTCATTTTCTTT
1 CTCTTTTTCATT
* ** *
262878 TTCACTCTCATT
1 CTCTTTTTCATT
262890 CTCTTTTTC
1 CTCTTTTTC
262899 TTTTTCTTTC
Statistics
Matches: 33, Mismatches: 12, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.11, C:0.28, G:0.00, T:0.61
Consensus pattern (12 bp):
CTCTTTTTCATT
Found at i:262870 original size:18 final size:18
Alignment explanation
Indices: 262849--262898 Score: 82
Period size: 18 Copynumber: 2.8 Consensus size: 18
262839 AAACTCTTTT
262849 TCATTCTCTTTTTCAATC
1 TCATTCTCTTTTTCAATC
* *
262867 TCATTTTCTTTTTCACTC
1 TCATTCTCTTTTTCAATC
262885 TCATTCTCTTTTTC
1 TCATTCTCTTTTTC
262899 TTTTTCTTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TCATTCTCTTTTTCAATC
Found at i:262957 original size:42 final size:42
Alignment explanation
Indices: 262902--262998 Score: 142
Period size: 42 Copynumber: 2.3 Consensus size: 42
262892 CTTTTTCTTT
* * * *
262902 TTCTTTCA-TTTCTTTGTTTCTTTTCTTGATTTCATTCAAGA
1 TTCTCTCATTTTCTTTGTTTCTTCTCTCGATTTCATTCAAAA
262943 TTCTCTCATTTTCTTTGTTTCTTCTCTCGATTTCATTCAAAA
1 TTCTCTCATTTTCTTTGTTTCTTCTCTCGATTTCATTCAAAA
*
262985 TCCTCTCATTTTCT
1 TTCTCTCATTTTCT
262999 CTCATAATCT
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
41 7 0.14
42 43 0.86
ACGTcount: A:0.14, C:0.23, G:0.05, T:0.58
Consensus pattern (42 bp):
TTCTCTCATTTTCTTTGTTTCTTCTCTCGATTTCATTCAAAA
Found at i:267848 original size:18 final size:18
Alignment explanation
Indices: 267827--267876 Score: 82
Period size: 18 Copynumber: 2.8 Consensus size: 18
267817 AAAATCTTTT
267827 TCATTCTCTTTTTCAATC
1 TCATTCTCTTTTTCAATC
* *
267845 TCATTTTCTTTTTCACTC
1 TCATTCTCTTTTTCAATC
267863 TCATTCTCTTTTTC
1 TCATTCTCTTTTTC
267877 TTTTTCTTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TCATTCTCTTTTTCAATC
Found at i:267935 original size:42 final size:41
Alignment explanation
Indices: 267880--267973 Score: 143
Period size: 42 Copynumber: 2.3 Consensus size: 41
267870 CTTTTTCTTT
* * *
267880 TTCTTTCATTTCTTTGTTTCTTTTCTCGATTTCATTCAAGA
1 TTCTCTCATTTCTTTGTTTCTTCTCTCGATTTCATTCAAAA
267921 TTCTCTCACTTTCTTTGTTTCTTCTCTCGATTTCATTCAAAA
1 TTCTCTCA-TTTCTTTGTTTCTTCTCTCGATTTCATTCAAAA
*
267963 TCCTCTCATTT
1 TTCTCTCATTT
267974 TCTCTCATAA
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
41 10 0.21
42 38 0.79
ACGTcount: A:0.15, C:0.24, G:0.05, T:0.55
Consensus pattern (41 bp):
TTCTCTCATTTCTTTGTTTCTTCTCTCGATTTCATTCAAAA
Found at i:267954 original size:21 final size:21
Alignment explanation
Indices: 267887--267954 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
267877 TTTTTCTTTC
*
267887 ATTTCTTTGTTTCTTTTCTCG
1 ATTTCTTTGTTTCTTCTCTCG
* *****
267908 ATTTCATTCAAGATTCTCTC-
1 ATTTCTTTGTTTCTTCTCTCG
267928 ACTTTCTTTGTTTCTTCTCTCG
1 A-TTTCTTTGTTTCTTCTCTCG
267950 ATTTC
1 ATTTC
267955 ATTCAAAATC
Statistics
Matches: 32, Mismatches: 13, Indels: 4
0.65 0.27 0.08
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.12, C:0.24, G:0.07, T:0.57
Consensus pattern (21 bp):
ATTTCTTTGTTTCTTCTCTCG
Found at i:268639 original size:30 final size:29
Alignment explanation
Indices: 268544--268640 Score: 79
Period size: 30 Copynumber: 3.2 Consensus size: 29
268534 AGCTCACTCC
* *
268544 TAGCTC-ACTTTCAACTCACGAGATAAACCT
1 TAGCTCAACTTT-AGCTCACGAG-TAAAGCT
* * * **
268574 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGTAAAG-CT
*
268604 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAG-TAAAGCT
268634 TAGCTCA
1 TAGCTCA
268641 GTTTAGTTTA
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 41 0.82
31 7 0.14
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (29 bp):
TAGCTCAACTTTAGCTCACGAGTAAAGCT
Found at i:272605 original size:15 final size:15
Alignment explanation
Indices: 272585--272613 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
272575 AAATTACAAC
272585 TTGAATTTTTTTAAT
1 TTGAATTTTTTTAAT
272600 TTGAATTTTTTTAA
1 TTGAATTTTTTTAA
272614 CTACGAACCT
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:0.28, C:0.00, G:0.07, T:0.66
Consensus pattern (15 bp):
TTGAATTTTTTTAAT
Found at i:273846 original size:19 final size:19
Alignment explanation
Indices: 273822--273859 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
273812 ATAACTAAAC
273822 AATTTA-ACAGCAATAATTA
1 AATTTAGACA-CAATAATTA
*
273841 AATTTAGACATAATAATTA
1 AATTTAGACACAATAATTA
273860 TAAGTCAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.53, C:0.08, G:0.05, T:0.34
Consensus pattern (19 bp):
AATTTAGACACAATAATTA
Found at i:274042 original size:20 final size:20
Alignment explanation
Indices: 273996--274043 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
273986 AGTAAGCTCG
273996 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
*** * *
274016 AACGAGCTTAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
274036 GTTGAGCT
1 GTTGAGCT
274044 GGACGGAGCT
Statistics
Matches: 20, Mismatches: 8, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.31, C:0.17, G:0.29, T:0.23
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:275825 original size:20 final size:20
Alignment explanation
Indices: 275779--275826 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
275769 AGTAAGCTCG
275779 GTTGAGCTCAAACCAGCTGA
1 GTTGAGCTCAAACCAGCTGA
*** **
275799 AACGAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACCAGCTGA
275819 GTTGAGCT
1 GTTGAGCT
275827 GGACGGAGCT
Statistics
Matches: 20, Mismatches: 8, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.31, C:0.21, G:0.27, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACCAGCTGA
Found at i:276647 original size:22 final size:21
Alignment explanation
Indices: 276614--276655 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
276604 TCAAACCTAC
276614 ACAAGCATGCAAAATTTACACA
1 ACAAGCATGCAAAA-TTACACA
*
276636 ACAAGGCA-GCAACATTACAC
1 ACAA-GCATGCAAAATTACAC
276656 CACCATCACA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 6 0.33
22 9 0.50
23 3 0.17
ACGTcount: A:0.48, C:0.26, G:0.12, T:0.14
Consensus pattern (21 bp):
ACAAGCATGCAAAATTACACA
Found at i:280525 original size:30 final size:30
Alignment explanation
Indices: 280491--280587 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
280481 AGCTCACTCC
*
280491 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTCAGCTCACGAGATAAACCT
* * * * *
280521 TAGCTCAACTTCAGCTTAGGAGTTTAATCT
1 TAGCTCAACTTCAGCTCACGAGATAAACCT
* * *
280551 CAGCTCAACTTTAGCTCACGAGATAAAGCT
1 TAGCTCAACTTCAGCTCACGAGATAAACCT
280581 TAGCTCA
1 TAGCTCA
280588 TTTTAGTTTA
Statistics
Matches: 53, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
29 1 0.02
30 52 0.98
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGATAAACCT
Found at i:283175 original size:16 final size:15
Alignment explanation
Indices: 283154--283193 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
283144 ACATTCTTGT
283154 AAAGAAAAAACAAAGA
1 AAAGAAAAAACAAA-A
*
283170 AAAGAAAAAGCAAAA
1 AAAGAAAAAACAAAA
*
283185 GAAGAAAAA
1 AAAGAAAAA
283194 GAAAATGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.80, C:0.05, G:0.15, T:0.00
Consensus pattern (15 bp):
AAAGAAAAAACAAAA
Found at i:283186 original size:12 final size:11
Alignment explanation
Indices: 283154--283216 Score: 53
Period size: 11 Copynumber: 5.9 Consensus size: 11
283144 ACATTCTTGT
283154 AAAGAAAA-AA
1 AAAGAAAAGAA
283164 CAAAGAAAAGAA
1 -AAAGAAAAGAA
283176 AAAGCAAAAG-A
1 AAAG-AAAAGAA
*
283187 AGA-AAAAGAA
1 AAAGAAAAGAA
* *
283197 AATG-AAATAA
1 AAAGAAAAGAA
283207 AAAGAAAAGA
1 AAAGAAAAGA
283217 GAGGCAAGAG
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
9 5 0.12
10 10 0.24
11 19 0.46
12 7 0.17
ACGTcount: A:0.78, C:0.03, G:0.16, T:0.03
Consensus pattern (11 bp):
AAAGAAAAGAA
Found at i:283189 original size:15 final size:14
Alignment explanation
Indices: 283171--283216 Score: 56
Period size: 16 Copynumber: 3.1 Consensus size: 14
283161 AAACAAAGAA
283171 AAGAAAAAGCAAAAG
1 AAGAAAAAG-AAAAG
283186 AAGAAAAAGAAAATG
1 AAGAAAAAGAAAA-G
*
283201 AAATAAAAAGAAAAG
1 -AAGAAAAAGAAAAG
283216 A
1 A
283217 GAGGCAAGAG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 5 0.18
15 11 0.39
16 12 0.43
ACGTcount: A:0.76, C:0.02, G:0.17, T:0.04
Consensus pattern (14 bp):
AAGAAAAAGAAAAG
Found at i:283317 original size:24 final size:24
Alignment explanation
Indices: 283290--283352 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
283280 AAAACAAAAA
*
283290 GAAAAAGAAAAAGAAAATGAGATT
1 GAAAAAGAAAAAGAAAAAGAGATT
* * *
283314 GAAAAAGAGAATGAAAAAGAGTTT
1 GAAAAAGAAAAAGAAAAAGAGATT
* *
283338 GAGAGAGAAAAAGAA
1 GAAAAAGAAAAAGAA
283353 TGTGAACAAG
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.63, C:0.00, G:0.25, T:0.11
Consensus pattern (24 bp):
GAAAAAGAAAAAGAAAAAGAGATT
Found at i:283319 original size:13 final size:12
Alignment explanation
Indices: 283290--283334 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
283280 AAAACAAAAA
* *
283290 GAAAAAGAAAAA
1 GAAAAAGAGAAT
* *
283302 GAAAATGAGATT
1 GAAAAAGAGAAT
283314 GAAAAAGAGAAT
1 GAAAAAGAGAAT
283326 GAAAAAGAG
1 GAAAAAGAG
283335 TTTGAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.24, T:0.09
Consensus pattern (12 bp):
GAAAAAGAGAAT
Found at i:286075 original size:20 final size:20
Alignment explanation
Indices: 286029--286076 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
286019 AGTAAGCTCG
286029 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
*** * *
286049 AACGAGCTTAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
286069 GTTGAGCT
1 GTTGAGCT
286077 GGACGGAGCT
Statistics
Matches: 20, Mismatches: 8, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.31, C:0.17, G:0.29, T:0.23
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:287344 original size:11 final size:12
Alignment explanation
Indices: 287312--287344 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
287302 GAGCTGTAGC
287312 AAACTTAATTAT
1 AAACTTAATTAT
*
287324 AAACTGAATTA-
1 AAACTTAATTAT
287335 AAACTTAATT
1 AAACTTAATT
287345 TATTAGAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 9 0.47
12 10 0.53
ACGTcount: A:0.52, C:0.09, G:0.03, T:0.36
Consensus pattern (12 bp):
AAACTTAATTAT
Found at i:287419 original size:20 final size:21
Alignment explanation
Indices: 287376--287422 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
287366 AGCTGAATCA
*
287376 AGCTGAATTCTAGCTCAAACG
1 AGCTGAATTCGAGCTCAAACG
**
287397 AGCTGAA-TCGAGCTCAAGTG
1 AGCTGAATTCGAGCTCAAACG
287417 AGCTGA
1 AGCTGA
287423 TGGGAGCTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 16 0.70
21 7 0.30
ACGTcount: A:0.32, C:0.21, G:0.26, T:0.21
Consensus pattern (21 bp):
AGCTGAATTCGAGCTCAAACG
Found at i:288928 original size:30 final size:29
Alignment explanation
Indices: 288894--288965 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 29
288884 AGCTCACTCC
*
288894 TAGCTCACTTTCAACTCATGAGCTAAACCT
1 TAGCTCACTTT-AACTCACGAGCTAAACCT
* *
288924 TAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTC-ACTTTAACTCACGAGCTAAACCT
*
288954 TAGCTCATTTTA
1 TAGCTCACTTTA
288966 GTTTAAACTC
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
29 5 0.14
30 27 0.73
31 5 0.14
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.32
Consensus pattern (29 bp):
TAGCTCACTTTAACTCACGAGCTAAACCT
Found at i:296322 original size:56 final size:56
Alignment explanation
Indices: 296217--296323 Score: 153
Period size: 56 Copynumber: 1.9 Consensus size: 56
296207 ATTAATGCCG
* * * * *
296217 TCCATGCATGGTGAATATCTCATTTAATTCATGTTTTGCTTCCCTTTAAATTCCGT
1 TCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCACATTAAATTCCGT
296273 TCCATACATGG-GAACATCTCATTTAATTCATGTCTTTGCTGCACATTAAAT
1 TCCATACATGGTGAACATCTCATTTAATTCATGT-TTTGCTGCACATTAAAT
296324 CAGCAAGCAG
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
55 21 0.47
56 24 0.53
ACGTcount: A:0.25, C:0.21, G:0.12, T:0.41
Consensus pattern (56 bp):
TCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCACATTAAATTCCGT
Found at i:296972 original size:20 final size:20
Alignment explanation
Indices: 296947--297001 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
296937 ACGAGTTAAA
* *
296947 TTGAGCTTGAATGAGCTGAC
1 TTGAGCTCGAATGAGCTAAC
*
296967 TTGAGCACGAATGAGCTAAC
1 TTGAGCTCGAATGAGCTAAC
296987 TTGAGCTCGAATGAG
1 TTGAGCTCGAATGAG
297002 TTGAACCACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.25
Consensus pattern (20 bp):
TTGAGCTCGAATGAGCTAAC
Found at i:298325 original size:15 final size:16
Alignment explanation
Indices: 298286--298326 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
298276 AACAACACTC
298286 CTTTCTTTTTCACTTT
1 CTTTCTTTTTCACTTT
* *
298302 C-ATCCTTTTCA-TTT
1 CTTTCTTTTTCACTTT
298316 CTTTCTTTTTC
1 CTTTCTTTTTC
298327 CAACTCATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 3
0.74 0.15 0.11
Matches are distributed among these distances:
14 4 0.20
15 15 0.75
16 1 0.05
ACGTcount: A:0.07, C:0.27, G:0.00, T:0.66
Consensus pattern (16 bp):
CTTTCTTTTTCACTTT
Found at i:299663 original size:56 final size:55
Alignment explanation
Indices: 299547--299664 Score: 159
Period size: 55 Copynumber: 2.1 Consensus size: 55
299537 TGCATGCTTT
* * * *
299547 CATT-AATGCCGTCCATGCATGGTGAATATCTCATTTAATTCATGTTTTGCTTCC
1 CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
*
299601 CTTTAAATGCCGTTCCATACATGG-GAACATCTCATTTAATTCATGTCTTTGCTGCA
1 CATTAAATGCCG-TCCATACATGGTGAACATCTCATTTAATTCATGT-TTTGCTGCA
299657 CATTAAAT
1 CATTAAAT
299665 CAGCAAGCAG
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
54 3 0.05
55 28 0.51
56 24 0.44
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (55 bp):
CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
Found at i:300313 original size:20 final size:20
Alignment explanation
Indices: 300288--300342 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
300278 ACGAGTTAAA
* *
300288 TTGAGCTTGAATGAGCTGAC
1 TTGAGCTCGAATGAGCTAAC
*
300308 TTGAGCACGAATGAGCTAAC
1 TTGAGCTCGAATGAGCTAAC
300328 TTGAGCTCGAATGAG
1 TTGAGCTCGAATGAG
300343 TTGAACCACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.25
Consensus pattern (20 bp):
TTGAGCTCGAATGAGCTAAC
Found at i:300935 original size:30 final size:30
Alignment explanation
Indices: 300901--300978 Score: 77
Period size: 30 Copynumber: 2.6 Consensus size: 30
300891 TAAACTAAAA
*
300901 TGAGCTAAGCTTTAGCTCATGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCATAAGCTAAAGT
* * * * *
300931 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCATAAGCTAAAGT
*
300961 TGAGCTAAGGTTTAGCTC
1 TGAGCTAAGCTTTAGCTC
300979 GTGAATTGAA
Statistics
Matches: 36, Mismatches: 10, Indels: 4
0.72 0.20 0.08
Matches are distributed among these distances:
29 2 0.06
30 31 0.86
31 3 0.08
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCATAAGCTAAAGT
Found at i:303148 original size:248 final size:248
Alignment explanation
Indices: 302708--303204 Score: 807
Period size: 248 Copynumber: 2.0 Consensus size: 248
302698 AAAAAAGTTC
* * * *
302708 TTGTAACACCTCTTACCAATACCCGAGGCCGGGATAAGGTACGAGGTGTTACTGGACAAACATAC
1 TTGTAACACCCCTTACCAATACCCGACGCCGGGATAAGGTACGAGGTGCTACCGGACAAACATAC
* * *
302773 AAACATTAAACTAAAATACGGGCCATAAAATTTTATTCATATTTCAAAACGTTCATTCACTTACA
66 AAACATTAAACTAAAATACGAGCCATAAAATTTCATTCATATTTCAAAACATTCATTCACTTACA
* * *
302838 CATAGTCCCTTATTTGAGTCTATGAAGCCCAAAACATACTTTAGAAAGTGTTCGGGACTAAACCG
131 CATAGTCCCTTATTTGAGTCTACGAAGCCCAAAACATACTTTAGAAAGGGTTCGGAACTAAACCG
*
302903 AGAACTTACAAAAATCTTGGAAATTTCATGCTTTAAGGCTCCACACGCCCGTG
196 AGAACTTACAAAAATCTTGGAAATTTCATACTTTAAGGCTCCACACGCCCGTG
** *
302956 TTGTAACACCCCTTACCTGTACCCGACGCTGGGATAAGGTACGAGGCT-CTACCGGACAAACATA
1 TTGTAACACCCCTTACCAATACCCGACGCCGGGATAAGGTACGAGG-TGCTACCGGACAAACATA
* *
303020 CAAATATTAAACTAAAATACGAGCCATAAAATTTCATTCATATTTCAAAGCATTCATTCACTTAC
65 CAAACATTAAACTAAAATACGAGCCATAAAATTTCATTCATATTTCAAAACATTCATTCACTTAC
* * *
303085 ACATAGTCCTTTATTTGAGTTTACGGAGCCCAAAACATACTTTAGAAAGGGTTCGGAACTAAACC
130 ACATAGTCCCTTATTTGAGTCTACGAAGCCCAAAACATACTTTAGAAAGGGTTCGGAACTAAACC
303150 GAGAACTTACAAAAATCTTGGAAATTTCATACTTTAAGGCTCCACACGCCCGTG
195 GAGAACTTACAAAAATCTTGGAAATTTCATACTTTAAGGCTCCACACGCCCGTG
303204 T
1 T
303205 CCCAAAGTCG
Statistics
Matches: 229, Mismatches: 19, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
248 228 1.00
249 1 0.00
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.27
Consensus pattern (248 bp):
TTGTAACACCCCTTACCAATACCCGACGCCGGGATAAGGTACGAGGTGCTACCGGACAAACATAC
AAACATTAAACTAAAATACGAGCCATAAAATTTCATTCATATTTCAAAACATTCATTCACTTACA
CATAGTCCCTTATTTGAGTCTACGAAGCCCAAAACATACTTTAGAAAGGGTTCGGAACTAAACCG
AGAACTTACAAAAATCTTGGAAATTTCATACTTTAAGGCTCCACACGCCCGTG
Found at i:309184 original size:21 final size:21
Alignment explanation
Indices: 309160--309227 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
309150 GATTTTGAAT
309160 GAAATCGAGAGAAGAAACAAA
1 GAAATCGAGAGAAGAAACAAA
***** *
309181 GAAAAT-GAGAGAATCTTGAAT
1 G-AAATCGAGAGAAGAAACAAA
*
309202 GAAATCGAGAAAAGAAACAAA
1 GAAATCGAGAGAAGAAACAAA
309223 GAAAT
1 GAAAT
309228 GAAAGAAAAA
Statistics
Matches: 32, Mismatches: 13, Indels: 4
0.65 0.27 0.08
Matches are distributed among these distances:
20 4 0.12
21 24 0.75
22 4 0.12
ACGTcount: A:0.59, C:0.07, G:0.22, T:0.12
Consensus pattern (21 bp):
GAAATCGAGAGAAGAAACAAA
Found at i:309200 original size:42 final size:42
Alignment explanation
Indices: 309138--309234 Score: 151
Period size: 42 Copynumber: 2.3 Consensus size: 42
309128 AGATTATGAG
* * *
309138 AGAAAATGAGAGGATTTTGAATGAAATCGAGAGAAGAAACAA
1 AGAAAATGAGAGAATCTTGAATGAAATCGAGAAAAGAAACAA
309180 AGAAAATGAGAGAATCTTGAATGAAATCGAGAAAAGAAACAA
1 AGAAAATGAGAGAATCTTGAATGAAATCGAGAAAAGAAACAA
*
309222 AG-AAATGAAAGAA
1 AGAAAATGAGAGAA
309235 AAAGAAAAAG
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
41 10 0.20
42 41 0.80
ACGTcount: A:0.57, C:0.05, G:0.24, T:0.14
Consensus pattern (42 bp):
AGAAAATGAGAGAATCTTGAATGAAATCGAGAAAAGAAACAA
Found at i:309261 original size:18 final size:18
Alignment explanation
Indices: 309238--309287 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
309228 GAAAGAAAAA
*
309238 GAAAAAGAGATTGAGAGT
1 GAAAAAGAGAATGAGAGT
* *
309256 GAAAAAGAAAATGAGATT
1 GAAAAAGAGAATGAGAGT
309274 GAAAAAGAGAATGA
1 GAAAAAGAGAATGA
309288 AAAAGAGTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.58, C:0.00, G:0.28, T:0.14
Consensus pattern (18 bp):
GAAAAAGAGAATGAGAGT
Found at i:309264 original size:24 final size:24
Alignment explanation
Indices: 309231--309312 Score: 101
Period size: 24 Copynumber: 3.4 Consensus size: 24
309221 AAGAAATGAA
309231 AGAAAAAGAAAAAGAGATTGAGAG
1 AGAAAAAGAAAAAGAGATTGAGAG
* * * *
309255 TGAAAAAGAAAATGAGATTGAAAA
1 AGAAAAAGAAAAAGAGATTGAGAG
* * *
309279 AGAGAATGAAAAAGAGTTTGAGAG
1 AGAAAAAGAAAAAGAGATTGAGAG
309303 AGAAAAAGAA
1 AGAAAAAGAA
309313 TGTGAACAAG
Statistics
Matches: 45, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.61, C:0.00, G:0.27, T:0.12
Consensus pattern (24 bp):
AGAAAAAGAAAAAGAGATTGAGAG
Found at i:309326 original size:48 final size:48
Alignment explanation
Indices: 309229--309349 Score: 120
Period size: 48 Copynumber: 2.5 Consensus size: 48
309219 CAAAGAAATG
* * * **
309229 AAAGAAAAAGAAAAAGAGATTGAGAGTGAAAAAGAAAATGAGATTGAA
1 AAAGAGAATGAAAAAGAGATTGAGAGAGAAAAAGAAAATGAGAAAGAA
* **
309277 AAAGAGAATGAAAAAGAGTTTGAGAGAGAAAAAGAATGTGA-ACAAGAA
1 AAAGAGAATGAAAAAGAGATTGAGAGAGAAAAAGAAAATGAGA-AAGAA
* *
309325 AAA-AGAGTGGAAAAAGAAATTGAGA
1 AAAGAGAAT-GAAAAAGAGATTGAGA
309350 TAAAAGAAAC
Statistics
Matches: 60, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
47 5 0.08
48 55 0.92
ACGTcount: A:0.60, C:0.01, G:0.26, T:0.12
Consensus pattern (48 bp):
AAAGAGAATGAAAAAGAGATTGAGAGAGAAAAAGAAAATGAGAAAGAA
Found at i:309341 original size:18 final size:19
Alignment explanation
Indices: 309305--309343 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
309295 TTTGAGAGAG
*
309305 AAAAAGAATGTGAACAAGA
1 AAAAAGAATGTGAAAAAGA
*
309324 AAAAAGAGTG-GAAAAAGA
1 AAAAAGAATGTGAAAAAGA
309342 AA
1 AA
309344 TTGAGATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.67, C:0.03, G:0.23, T:0.08
Consensus pattern (19 bp):
AAAAAGAATGTGAAAAAGA
Found at i:310948 original size:10 final size:10
Alignment explanation
Indices: 310935--310959 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
310925 AGCTCAACTC
310935 AGCTCGTTTG
1 AGCTCGTTTG
310945 AGCTCGTTTG
1 AGCTCGTTTG
310955 AGCTC
1 AGCTC
310960 AACTGAGCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.12, C:0.24, G:0.28, T:0.36
Consensus pattern (10 bp):
AGCTCGTTTG
Done.