Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold19
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: 2266706
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 17655 characters in sequence are not A, C, G, or T
File 2 of 15
Found at i:123145 original size:13 final size:13
Alignment explanation
Indices: 123127--123151 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
123117 TAATAACTTT
123127 GTATATAATTTTA
1 GTATATAATTTTA
123140 GTATATAATTTT
1 GTATATAATTTT
123152 TAACCTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (13 bp):
GTATATAATTTTA
Found at i:124867 original size:20 final size:19
Alignment explanation
Indices: 124806--124870 Score: 61
Period size: 20 Copynumber: 3.6 Consensus size: 19
124796 ACTATACGAA
*
124806 TATATACATTTATTAAAATT
1 TATATA-ATATATTAAAATT
124826 TATATAA-A-A-T-AAA-T
1 TATATAATATATTAAAATT
124840 TAT-TAATATATTAAAATT
1 TATATAATATATTAAAATT
124858 TATATAAATATAT
1 TATAT-AATATAT
124871 AACATTATAA
Statistics
Matches: 37, Mismatches: 1, Indels: 14
0.71 0.02 0.27
Matches are distributed among these distances:
13 3 0.08
14 5 0.14
15 4 0.11
16 2 0.05
17 4 0.11
18 4 0.11
19 2 0.05
20 13 0.35
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (19 bp):
TATATAATATATTAAAATT
Found at i:129954 original size:24 final size:25
Alignment explanation
Indices: 129926--129993 Score: 86
Period size: 25 Copynumber: 2.8 Consensus size: 25
129916 TAAAAATTAA
*
129926 CCACCAATTTTGACAAA-CAACAAG
1 CCACCAATTTTGACAAATAAACAAG
129950 CCACCAATTTTGACAAATAAACAAG
1 CCACCAATTTTGACAAATAAACAAG
* *
129975 CCTCC-ATATTTAACAAATA
1 CCACCAAT-TTTGACAAATA
129994 CAAAGGAAAC
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
24 19 0.49
25 20 0.51
ACGTcount: A:0.46, C:0.26, G:0.06, T:0.22
Consensus pattern (25 bp):
CCACCAATTTTGACAAATAAACAAG
Found at i:130051 original size:24 final size:24
Alignment explanation
Indices: 129923--130051 Score: 89
Period size: 24 Copynumber: 5.0 Consensus size: 24
129913 TAATAAAAAT
*
129923 TAACCACCAATTTTGACAAACAACA
1 TAACCACCATTTTTGACAAACAA-A
* * *
129948 -AGCCACCAATTTTGACAAATAAA
1 TAACCACCATTTTTGACAAACAAA
* * * *
129971 CAAGCCTCCATATTTAACAAATACAAA
1 TAA-CCACCATTTTTGAC-AA-ACAAA
*
129998 GGAAACCACCATTTTTGACAAACACAAAA
1 --TAACCACCATTTTTGAC-AA-AC-AAA
130027 TAACCACCATTTTTGACAAACAAA
1 TAACCACCATTTTTGACAAACAAA
130051 T
1 T
130052 GGGTGGCTTT
Statistics
Matches: 83, Mismatches: 14, Indels: 15
0.74 0.12 0.13
Matches are distributed among these distances:
23 1 0.01
24 25 0.30
25 12 0.14
26 4 0.05
27 20 0.24
28 16 0.19
29 5 0.06
ACGTcount: A:0.47, C:0.25, G:0.06, T:0.22
Consensus pattern (24 bp):
TAACCACCATTTTTGACAAACAAA
Found at i:132524 original size:28 final size:27
Alignment explanation
Indices: 132469--132534 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
132459 GCCACCTATT
*
132469 TGTTTGTCAAAAATGGTAGTTATTTTG
1 TGTTTGTCAAAAATAGTAGTTATTTTG
*
132496 TGTTCGTCAAAAATAGTAGTT-TCCTTTG
1 TGTTTGTCAAAAATAGTAGTTAT--TTTG
*
132524 TATTTGTCAAA
1 TGTTTGTCAAA
132535 TATGGAGGCT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
26 1 0.03
27 19 0.58
28 13 0.39
ACGTcount: A:0.27, C:0.09, G:0.18, T:0.45
Consensus pattern (27 bp):
TGTTTGTCAAAAATAGTAGTTATTTTG
Found at i:132646 original size:20 final size:20
Alignment explanation
Indices: 132623--132660 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
132613 GGCTCCCTCC
132623 TCCCTCTCAAGTATCCCTTA
1 TCCCTCTCAAGTATCCCTTA
**
132643 TCCCTCTCTTGTATCCCT
1 TCCCTCTCAAGTATCCCT
132661 CTTCAATTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.42, G:0.05, T:0.39
Consensus pattern (20 bp):
TCCCTCTCAAGTATCCCTTA
Found at i:135143 original size:21 final size:22
Alignment explanation
Indices: 135114--135159 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
135104 TGTTCAGACA
** *
135114 AGTAGTACTCCGCAGCAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
135136 AGTA-TACTCCAAAACAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
135157 AGT
1 AGT
135160 TTCAACAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (22 bp):
AGTAGTACTCCAAAACAGGTGG
Found at i:136232 original size:35 final size:35
Alignment explanation
Indices: 136186--136254 Score: 138
Period size: 35 Copynumber: 2.0 Consensus size: 35
136176 AACATGTAAG
136186 TACCCCACTTGCTTCTCATTTGAAACTTAGTGCTA
1 TACCCCACTTGCTTCTCATTTGAAACTTAGTGCTA
136221 TACCCCACTTGCTTCTCATTTGAAACTTAGTGCT
1 TACCCCACTTGCTTCTCATTTGAAACTTAGTGCT
136255 CACTTATCTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.22, C:0.29, G:0.12, T:0.38
Consensus pattern (35 bp):
TACCCCACTTGCTTCTCATTTGAAACTTAGTGCTA
Found at i:137132 original size:28 final size:27
Alignment explanation
Indices: 137077--137142 Score: 98
Period size: 27 Copynumber: 2.4 Consensus size: 27
137067 GCCACCCATT
137077 TATTTGTCAAAAATGGTGGTTATTTTG
1 TATTTGTCAAAAATGGTGGTTATTTTG
*
137104 TGTTTGTCAAAAATGGTGGTT-TCCTTTG
1 TATTTGTCAAAAATGGTGGTTAT--TTTG
137132 TATTTGTCAAA
1 TATTTGTCAAA
137143 TATAGAGACT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
26 1 0.03
27 20 0.57
28 14 0.40
ACGTcount: A:0.24, C:0.08, G:0.21, T:0.47
Consensus pattern (27 bp):
TATTTGTCAAAAATGGTGGTTATTTTG
Found at i:137253 original size:20 final size:20
Alignment explanation
Indices: 137230--137267 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
137220 GGCTCCCTCC
137230 TCCCTCTCAAGTATCCCTTA
1 TCCCTCTCAAGTATCCCTTA
**
137250 TCCCTCTCTTGTATCCCT
1 TCCCTCTCAAGTATCCCT
137268 CTTCAATTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.42, G:0.05, T:0.39
Consensus pattern (20 bp):
TCCCTCTCAAGTATCCCTTA
Found at i:139356 original size:31 final size:32
Alignment explanation
Indices: 139311--139377 Score: 100
Period size: 31 Copynumber: 2.1 Consensus size: 32
139301 TTATGATTGC
*
139311 AATGATCTATAATAAAATTCACTATCATAATA
1 AATGATCTAAAATAAAATTCACTATCATAATA
* *
139343 AATGATC-AAAATAAAATTTATTATCATAATA
1 AATGATCTAAAATAAAATTCACTATCATAATA
139374 AATG
1 AATG
139378 TCGATCGAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
31 25 0.78
32 7 0.22
ACGTcount: A:0.52, C:0.09, G:0.04, T:0.34
Consensus pattern (32 bp):
AATGATCTAAAATAAAATTCACTATCATAATA
Found at i:140373 original size:20 final size:20
Alignment explanation
Indices: 140333--140369 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
140323 TTATATTCCC
140333 TTAAAAAAAATACTGCTATA
1 TTAAAAAAAATACTGCTATA
*
140353 TTAAATAAAA-ACTGCTA
1 TTAAAAAAAATACTGCTA
140370 ATATATATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.54, C:0.11, G:0.05, T:0.30
Consensus pattern (20 bp):
TTAAAAAAAATACTGCTATA
Found at i:141266 original size:6 final size:6
Alignment explanation
Indices: 141255--141282 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
141245 ATAAAATATA
141255 ATAATT ATAATT ATAATT ATAATT ATAA
1 ATAATT ATAATT ATAATT ATAATT ATAA
141283 AAAATTTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (6 bp):
ATAATT
Found at i:143085 original size:100 final size:99
Alignment explanation
Indices: 142923--143102 Score: 249
Period size: 100 Copynumber: 1.8 Consensus size: 99
142913 AATACATTTA
* *
142923 GAAAGATGATGATGTAGATGCCTTAAATGTCTTGAGTACTAAATCAGAATAATTTCTTCTTTTAA
1 GAAAGATGATGATGTAGATGCCTTAAATGTCTTGAGTACCAAATCAGAACAATTTCTTCTTTTAA
142988 AACAAAATAACTTCGGTCAAGCGTCCCTACATTC
66 AACAAAATAACTTCGGTCAAGCGTCCCTACATTC
* *
143022 GAAAGATGAT-ATTGT-GAATGCCTTAAGTGTCTTTTGTGTACCAAATCAG-ACAATTTCTTCTT
1 GAAAGATGATGA-TGTAG-ATGCCTTAAATGTC--TTGAGTACCAAATCAGAACAATTTCTTCTT
* *
143084 TTAGAACAAAGTAACTTCG
62 TTAAAACAAAATAACTTCG
143103 TTTGTCAATC
Statistics
Matches: 71, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
98 2 0.03
99 26 0.37
100 29 0.41
101 14 0.20
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (99 bp):
GAAAGATGATGATGTAGATGCCTTAAATGTCTTGAGTACCAAATCAGAACAATTTCTTCTTTTAA
AACAAAATAACTTCGGTCAAGCGTCCCTACATTC
Found at i:143209 original size:22 final size:22
Alignment explanation
Indices: 143187--143230 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
143177 AATAATAATT
*
143187 TTTAAAA-T-TTTTATTAATTA
1 TTTAAAATTATTTTATTAATAA
*
143207 TTTAAAATTATTTTATTAAAAA
1 TTTAAAATTATTTTATTAATAA
143229 TT
1 TT
143231 ATTAAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 7 0.35
21 1 0.05
22 12 0.60
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TTTAAAATTATTTTATTAATAA
Found at i:143228 original size:15 final size:15
Alignment explanation
Indices: 143204--143233 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
143194 TTTTTATTAA
*
143204 TTATTTAAAATTATT
1 TTATTAAAAATTATT
143219 TTATTAAAAATTATT
1 TTATTAAAAATTATT
143234 AAAAAATAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TTATTAAAAATTATT
Found at i:146294 original size:28 final size:29
Alignment explanation
Indices: 146262--146347 Score: 90
Period size: 28 Copynumber: 3.1 Consensus size: 29
146252 GGAGTTAGTC
* *
146262 AAATAATATTACATA-AATATAACATAAA
1 AAATAATATAACATATAACATAACATAAA
* * *
146290 AAATAAT-TAAAATATGACATGACATAAA
1 AAATAATATAACATATAACATAACATAAA
*
146318 AAATAATATGAC-TATAACATAA-ATAAA
1 AAATAATATAACATATAACATAACATAAA
146345 AAA
1 AAA
146348 ATATTAAAAT
Statistics
Matches: 47, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
27 13 0.28
28 32 0.68
29 2 0.04
ACGTcount: A:0.64, C:0.07, G:0.03, T:0.26
Consensus pattern (29 bp):
AAATAATATAACATATAACATAACATAAA
Found at i:146612 original size:3 final size:3
Alignment explanation
Indices: 146604--146630 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
146594 AATCTCACCA
146604 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
146631 GATGGGCTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:154947 original size:15 final size:15
Alignment explanation
Indices: 154929--154972 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
154919 TAAATACTTT
154929 TTATTTAAATTTTAA
1 TTATTTAAATTTTAA
* *
154944 TTATATAAATATTAA
1 TTATTTAAATTTTAA
*
154959 -TATTAAAATTTTAA
1 TTATTTAAATTTTAA
154973 CTTTTTTTAA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TTATTTAAATTTTAA
Found at i:155227 original size:19 final size:19
Alignment explanation
Indices: 155167--155228 Score: 56
Period size: 19 Copynumber: 3.2 Consensus size: 19
155157 AACAAACATG
*
155167 TTTAATACTTATTATATTCATA
1 TTTAATAATT-TT-TATT-ATA
* *
155189 TTTAA-AA-TTTTAATACA
1 TTTAATAATTTTTATTATA
155206 TTTAATAATTTTTATTATA
1 TTTAATAATTTTTATTATA
155225 TTTA
1 TTTA
155229 TATTTACAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
17 7 0.21
18 5 0.15
19 14 0.42
20 1 0.03
21 1 0.03
22 5 0.15
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTAATAATTTTTATTATA
Found at i:159575 original size:28 final size:29
Alignment explanation
Indices: 159538--159595 Score: 75
Period size: 28 Copynumber: 2.0 Consensus size: 29
159528 ATGGTGAGAA
159538 TAAAAAATAATTA-TTAAAA-ATATTAAAT
1 TAAAAAATAA-TAGTTAAAATATATTAAAT
* *
159566 TAAAATATAATAGTTAAAATTTATTAAAT
1 TAAAAAATAATAGTTAAAATATATTAAAT
159595 T
1 T
159596 TATATTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 2 0.08
28 15 0.58
29 9 0.35
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.40
Consensus pattern (29 bp):
TAAAAAATAATAGTTAAAATATATTAAAT
Found at i:159647 original size:28 final size:29
Alignment explanation
Indices: 159614--159681 Score: 102
Period size: 29 Copynumber: 2.4 Consensus size: 29
159604 TATCAAATAA
*
159614 TAAATATAAATT-AAAATTATATTTATAT
1 TAAATATAAATTAAAAATAATATTTATAT
*
159642 TAAATATTAATTAAAAATAATATTTATAT
1 TAAATATAAATTAAAAATAATATTTATAT
*
159671 TAAAAATAAAT
1 TAAATATAAAT
159682 AATTTAAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
28 11 0.31
29 24 0.69
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (29 bp):
TAAATATAAATTAAAAATAATATTTATAT
Found at i:159669 original size:35 final size:35
Alignment explanation
Indices: 159590--159671 Score: 94
Period size: 35 Copynumber: 2.3 Consensus size: 35
159580 TAAAATTTAT
* *
159590 TAAATTTATATTTTTATCAAATAATAAATATAAAT
1 TAAATTTATATTTATATCAAATAATAAATATAAAA
* * * *
159625 TAAAATTATATTTATATTAAATATTAATTA-AAAA
1 TAAATTTATATTTATATCAAATAATAAATATAAAA
159659 TAATATTTATATT
1 TAA-ATTTATATT
159672 AAAAATAAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
34 6 0.15
35 33 0.85
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (35 bp):
TAAATTTATATTTATATCAAATAATAAATATAAAA
Found at i:160181 original size:28 final size:29
Alignment explanation
Indices: 160137--160218 Score: 69
Period size: 32 Copynumber: 2.7 Consensus size: 29
160127 TAACTATTTT
*
160137 AAATATATTTTT-TATTATTTAAT-AATAA
1 AAAT-TATTTTTAAATTATTTAATAAATAA
160165 AAATTATTTTTAAATTAAATTTTAATAAATAA
1 AAATTATTTTTAAATT--A-TTTAATAAATAA
* *
160197 TAATTATTGATTTAACTTATTT
1 AAATTATT--TTTAAATTATTT
160219 TAAATTGTAA
Statistics
Matches: 44, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
27 7 0.16
28 7 0.16
30 1 0.02
31 9 0.20
32 13 0.30
34 7 0.16
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (29 bp):
AAATTATTTTTAAATTATTTAATAAATAA
Found at i:160219 original size:32 final size:30
Alignment explanation
Indices: 160154--160221 Score: 75
Period size: 32 Copynumber: 2.2 Consensus size: 30
160144 TTTTTTATTA
160154 TTTAATAATAAAAATTATTTTTAAATTAAAT
1 TTTAATAATAAAAATTATTTTTAAATT-AAT
* *
160185 TTTAATAAATAATAATTATTGATTTAACTT-AT
1 TTTAAT-AATAAAAATTATT--TTTAAATTAAT
160217 TTTAA
1 TTTAA
160222 ATTGTAATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
31 6 0.19
32 19 0.59
34 7 0.22
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (30 bp):
TTTAATAATAAAAATTATTTTTAAATTAAT
Found at i:160804 original size:24 final size:21
Alignment explanation
Indices: 160772--160863 Score: 75
Period size: 24 Copynumber: 4.2 Consensus size: 21
160762 AATACATAAT
*
160772 TTTTTTTTCTTTTCTCTCTTCTTC
1 TTTTCTTTCTTTTC-CT-TT-TTC
160796 TTTTCTTTCATTTTCCTTTTTC
1 TTTTCTTTC-TTTTCCTTTTTC
160818 --TTCTTTCTTTTCCTTTTGTCC
1 TTTTCTTTCTTTTCCTTTT-T-C
*
160839 TTTTTCCTTC-TTT-CTTTTTC
1 -TTTTCTTTCTTTTCCTTTTTC
160859 TTTTC
1 TTTTC
160864 CTATTTTCCC
Statistics
Matches: 60, Mismatches: 2, Indels: 17
0.76 0.03 0.22
Matches are distributed among these distances:
19 15 0.25
20 9 0.15
21 2 0.03
22 8 0.13
23 5 0.08
24 16 0.27
25 5 0.08
ACGTcount: A:0.01, C:0.25, G:0.01, T:0.73
Consensus pattern (21 bp):
TTTTCTTTCTTTTCCTTTTTC
Found at i:160809 original size:25 final size:24
Alignment explanation
Indices: 160772--160865 Score: 66
Period size: 25 Copynumber: 3.7 Consensus size: 24
160762 AATACATAAT
*
160772 TTTTTTTTCTTTT-CTCTCTTCTTC
1 TTTTCTTTCTTTTCCT-TCTTCTTC
*
160796 TTTTCTTTCATTTTCCTTTTTCTTC
1 TTTTCTTTC-TTTTCCTTCTTCTTC
*
160821 -TTTCTTTTCCTTTTGTCCTTTTTCCTTC
1 TTTTC-TTT-C-TTT-TCCTTCTT-CTTC
*
160849 TTTCTTTTTCTTTTCCT
1 TTT-TCTTTCTTTTCCT
160866 ATTTTCCCTT
Statistics
Matches: 58, Mismatches: 4, Indels: 14
0.76 0.05 0.18
Matches are distributed among these distances:
24 12 0.21
25 14 0.24
26 10 0.17
27 11 0.19
28 5 0.09
29 5 0.09
30 1 0.02
ACGTcount: A:0.01, C:0.26, G:0.01, T:0.72
Consensus pattern (24 bp):
TTTTCTTTCTTTTCCTTCTTCTTC
Found at i:160830 original size:19 final size:19
Alignment explanation
Indices: 160798--160871 Score: 70
Period size: 19 Copynumber: 4.0 Consensus size: 19
160788 TCTTCTTCTT
160798 TTCTTTCATTTTCCTTTTTC
1 TTCTTTC-TTTTCCTTTTTC
160818 TTCTTTCTTTTCCTTTTGTC
1 TTCTTTCTTTTCCTTTT-TC
160838 --C--T-TTTTCCTTCTTTC
1 TTCTTTCTTTTCCTT-TTTC
160853 TT-TTTCTTTTCCTATTTTC
1 TTCTTTCTTTTCCT-TTTTC
160872 CCTTCTTTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 17
0.73 0.00 0.27
Matches are distributed among these distances:
15 10 0.22
16 3 0.07
18 2 0.04
19 21 0.46
20 10 0.22
ACGTcount: A:0.03, C:0.26, G:0.01, T:0.70
Consensus pattern (19 bp):
TTCTTTCTTTTCCTTTTTC
Found at i:160870 original size:28 final size:26
Alignment explanation
Indices: 160772--160886 Score: 96
Period size: 28 Copynumber: 4.3 Consensus size: 26
160762 AATACATAAT
*
160772 TTTTTTTTC-TTTT-CTCTCTT-CTTC
1 TTTTTTTTCATTTTCCT-TTTTCCTTC
*
160796 TTTTCTTTCATTTTCCTTTTT-CTTC
1 TTTTTTTTCATTTTCCTTTTTCCTTC
* *
160821 TTTCTTTTCCTTTTGTCCTTTTTCCTTC
1 TTT-TTTTTCATTT-TCCTTTTTCCTTC
160849 TTTCTTTTTC-TTTTCCTATTTTCCCTTC
1 TTT-TTTTTCATTTTCCT-TTTT-CCTTC
160877 TTTTTCTTTC
1 TTTTT-TTTC
160887 TCCTTATCCC
Statistics
Matches: 77, Mismatches: 6, Indels: 12
0.81 0.06 0.13
Matches are distributed among these distances:
24 8 0.10
25 14 0.18
26 13 0.17
27 17 0.22
28 25 0.32
ACGTcount: A:0.02, C:0.26, G:0.01, T:0.71
Consensus pattern (26 bp):
TTTTTTTTCATTTTCCTTTTTCCTTC
Found at i:160884 original size:34 final size:34
Alignment explanation
Indices: 160806--160887 Score: 91
Period size: 34 Copynumber: 2.4 Consensus size: 34
160796 TTTTCTTTCA
*
160806 TTTTCCTT-TTTCTTCTTTCTTTTCCTTTTGTCC
1 TTTTTCTTCTTTCTTCTTTCTTTTCCTTTTGTCC
160839 TTTTTCCTTCTTTCTT-TTTCTTTTCCTATTT-TCCC
1 TTTTT-CTTCTTTCTTCTTTCTTTTCCT-TTTGT-CC
160874 TTCTTT-TTCTTTCT
1 TT-TTTCTTCTTTCT
160888 CCTTATCCCT
Statistics
Matches: 43, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
33 4 0.09
34 23 0.53
35 13 0.30
36 3 0.07
ACGTcount: A:0.01, C:0.27, G:0.01, T:0.71
Consensus pattern (34 bp):
TTTTTCTTCTTTCTTCTTTCTTTTCCTTTTGTCC
Found at i:160887 original size:28 final size:27
Alignment explanation
Indices: 160792--160879 Score: 101
Period size: 28 Copynumber: 3.3 Consensus size: 27
160782 TTTCTCTCTT
*
160792 CTTCTTT-TCTTTCATTTTCCTTTTT-
1 CTTCTTTCTTTTTCATTTTCCTTTTTC
* *
160817 CTTCTTTCTTTTCCTTTTGTCCTTTTTC
1 CTTCTTTCTTTTTCATTT-TCCTTTTTC
160845 CTTCTTTCTTTTTC-TTTTCCTATTTTCC
1 CTTCTTTCTTTTTCATTTTCCT-TTTT-C
160873 CTTCTTT
1 CTTCTTT
160880 TTCTTTCTCC
Statistics
Matches: 54, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
25 7 0.13
26 11 0.20
27 15 0.28
28 21 0.39
ACGTcount: A:0.02, C:0.27, G:0.01, T:0.69
Consensus pattern (27 bp):
CTTCTTTCTTTTTCATTTTCCTTTTTC
Found at i:160896 original size:23 final size:23
Alignment explanation
Indices: 160850--160899 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 23
160840 TTTTCCTTCT
*
160850 TTCTTTTTCTTTTCCTATTTTCCC
1 TTCTTTTTCTTTTCC-ATTATCCC
160874 TTCTTTTTCTTTCTCC-TTATCCC
1 TTCTTTTTCTTT-TCCATTATCCC
160897 TTC
1 TTC
160900 AAAAAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 9 0.38
24 12 0.50
25 3 0.12
ACGTcount: A:0.04, C:0.32, G:0.00, T:0.64
Consensus pattern (23 bp):
TTCTTTTTCTTTTCCATTATCCC
Found at i:161006 original size:17 final size:19
Alignment explanation
Indices: 160970--161009 Score: 57
Period size: 17 Copynumber: 2.2 Consensus size: 19
160960 AGTATTTATG
*
160970 TAAATTATTTATATGTATA
1 TAAATAATTTATATGTATA
160989 TAAATAATTT-TA-GTATA
1 TAAATAATTTATATGTATA
161006 TAAA
1 TAAA
161010 AAAACACAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 9 0.45
18 2 0.10
19 9 0.45
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (19 bp):
TAAATAATTTATATGTATA
Found at i:162946 original size:16 final size:16
Alignment explanation
Indices: 162926--162981 Score: 67
Period size: 16 Copynumber: 3.5 Consensus size: 16
162916 TTTTAAGCGA
162926 AAGTTATTCTAAATAT
1 AAGTTATTCTAAATAT
* *
162942 GAGTTATTTTAAATAT
1 AAGTTATTCTAAATAT
* *
162958 AAATTATTCTAAACAT
1 AAGTTATTCTAAATAT
*
162974 AAATTATT
1 AAGTTATT
162982 TTTAAAAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (16 bp):
AAGTTATTCTAAATAT
Found at i:162965 original size:32 final size:32
Alignment explanation
Indices: 162929--163018 Score: 94
Period size: 32 Copynumber: 2.8 Consensus size: 32
162919 TAAGCGAAAG
* *
162929 TTATTCTAAATATGAGTTATTTTAAATATAAA
1 TTATTCTAAATATAAGTTATTTTAAATAAAAA
* *
162961 TTATTCTAAACATAAATTATTTTTAAA-AAAAA
1 TTATTCTAAATATAAGTTA-TTTTAAATAAAAA
* * *
162993 TTGTTTTAAATGTAAGTT-TTTTAAAT
1 TTATTCTAAATATAAGTTATTTTAAAT
163019 GAGAATTTAT
Statistics
Matches: 47, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
30 7 0.15
32 33 0.70
33 7 0.15
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.48
Consensus pattern (32 bp):
TTATTCTAAATATAAGTTATTTTAAATAAAAA
Found at i:166555 original size:20 final size:20
Alignment explanation
Indices: 166519--166556 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
166509 AATTAACTTT
166519 AAATCATATTTAAAATATAA
1 AAATCATATTTAAAATATAA
*
166539 AAAT-ATATATTATAATAT
1 AAATCATAT-TTAAAATAT
166557 TTTAATGACA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (20 bp):
AAATCATATTTAAAATATAA
Found at i:167136 original size:20 final size:17
Alignment explanation
Indices: 167107--167152 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 17
167097 TAAAATTATA
167107 AATAAAAATTACAATTAAAT
1 AATAAAAATT-C-A-TAAAT
*
167127 AATCAAAATTCATAAAT
1 AATAAAAATTCATAAAT
167144 AATAAAAAT
1 AATAAAAAT
167153 AATCAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 13 0.54
18 1 0.04
19 1 0.04
20 9 0.38
ACGTcount: A:0.65, C:0.07, G:0.00, T:0.28
Consensus pattern (17 bp):
AATAAAAATTCATAAAT
Found at i:168084 original size:2 final size:2
Alignment explanation
Indices: 168077--168106 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
168067 AATTTTCATT
168077 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
168107 GATTAATAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:175949 original size:16 final size:17
Alignment explanation
Indices: 175924--175979 Score: 64
Period size: 16 Copynumber: 3.4 Consensus size: 17
175914 ATGTTTTTAA
175924 AAATTAATAAAAAATAT
1 AAATTAATAAAAAATAT
*
175941 AAATT-ATAAATAATCAT
1 AAATTAATAAAAAAT-AT
175958 --ATTAATAAAAAATAT
1 AAATTAATAAAAAATAT
175973 AATATTA
1 AA-ATTA
175980 TTATTTTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
15 5 0.16
16 16 0.50
17 7 0.22
18 4 0.12
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (17 bp):
AAATTAATAAAAAATAT
Found at i:176420 original size:24 final size:24
Alignment explanation
Indices: 176393--176439 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
176383 GAAATATTAT
*
176393 ATTTTTATAATTAATTTT-TTTTAA
1 ATTTTT-TAAATAATTTTATTTTAA
*
176417 ATTTTTTAAATATTTTTATTTTA
1 ATTTTTTAAATAATTTTATTTTA
176440 TTCATTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (24 bp):
ATTTTTTAAATAATTTTATTTTAA
Found at i:176839 original size:35 final size:36
Alignment explanation
Indices: 176776--176844 Score: 88
Period size: 35 Copynumber: 1.9 Consensus size: 36
176766 TATAATATTT
* *
176776 TTTATTTTTTAATAATTTAAATATAAAA-TAAAATA
1 TTTATTTTATAATAATTTAAATAAAAAATTAAAATA
*
176811 TTTATTTTAT-ATTATTTAAAATAAAAAATTAAAA
1 TTTATTTTATAATAATTT-AAATAAAAAATTAAAA
176845 ATAAATTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
34 6 0.21
35 18 0.62
36 5 0.17
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (36 bp):
TTTATTTTATAATAATTTAAATAAAAAATTAAAATA
Found at i:176980 original size:15 final size:15
Alignment explanation
Indices: 176940--176983 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
176930 AATTAAATTC
176940 AAATCAAATTTAAT-A
1 AAATC-AATTTAATCA
176955 AAA--AA-TTAATCA
1 AAATCAATTTAATCA
176967 AAATCAATTTAATCA
1 AAATCAATTTAATCA
176982 AA
1 AA
176984 TATTACTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
11 5 0.20
12 6 0.24
14 2 0.08
15 12 0.48
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (15 bp):
AAATCAATTTAATCA
Found at i:182278 original size:18 final size:19
Alignment explanation
Indices: 182251--182287 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
182241 TTTGGCGATC
182251 TAAT-ATTTTTATTTCAAA
1 TAATAATTTTTATTTCAAA
182269 TAATAATTTTTATTTCAAA
1 TAATAATTTTTATTTCAAA
182288 AACCAAAGCC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (19 bp):
TAATAATTTTTATTTCAAA
Found at i:182870 original size:18 final size:18
Alignment explanation
Indices: 182847--182891 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
182837 TTTAAACCCA
*
182847 ATTTTTAAATAATTTTAT
1 ATTTTTAAATAAATTTAT
**
182865 ATTTTTATTTAAATTTAT
1 ATTTTTAAATAAATTTAT
182883 -TTTTTAAAT
1 ATTTTTAAAT
182892 TTAATATTTT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
ATTTTTAAATAAATTTAT
Found at i:182899 original size:32 final size:29
Alignment explanation
Indices: 182857--182925 Score: 93
Period size: 32 Copynumber: 2.2 Consensus size: 29
182847 ATTTTTAAAT
*
182857 AATTTTATATTTTTATTTAAATTTATTTTTTA
1 AATTTAATATTTTTATTT-AA-TT-TTTTTTA
182889 AATTTAATATTTTTATTTAATTTTTTTTA
1 AATTTAATATTTTTATTTAATTTTTTTTA
182918 AATATTAA
1 AAT-TTAA
182926 ATAAATTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
29 10 0.29
30 6 0.17
31 2 0.06
32 17 0.49
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (29 bp):
AATTTAATATTTTTATTTAATTTTTTTTA
Found at i:182938 original size:30 final size:29
Alignment explanation
Indices: 182868--182938 Score: 72
Period size: 29 Copynumber: 2.3 Consensus size: 29
182858 ATTTTATATT
**
182868 TTTATTTAAATTTATTTTTTAAATTTAATATT
1 TTTATTT-AA-TT-TTTTTTAAATTTAATAAA
182900 TTTATTTAATTTTTTTTAAATATTAAATAAA
1 TTTATTTAATTTTTTTTAAAT-TT-AATAAA
182931 TTT-TTTAA
1 TTTATTTAA
182939 AAATAATTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
29 10 0.29
30 9 0.26
31 9 0.26
32 7 0.20
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (29 bp):
TTTATTTAATTTTTTTTAAATTTAATAAA
Found at i:183497 original size:16 final size:17
Alignment explanation
Indices: 183478--183519 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
183468 AAATTTCAAT
*
183478 ATTTATTTTTAATT-TA
1 ATTTATTTTTAATTCGA
183494 ATTTA-TTTTAATTCGA
1 ATTTATTTTTAATTCGA
183510 A-TTATTTTTA
1 ATTTATTTTTA
183520 TATAAATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 11 0.48
16 12 0.52
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (17 bp):
ATTTATTTTTAATTCGA
Found at i:184408 original size:18 final size:17
Alignment explanation
Indices: 184359--184426 Score: 58
Period size: 16 Copynumber: 4.2 Consensus size: 17
184349 AATATATATT
*
184359 TAAAATTTACAT-AATA
1 TAAAATTTATATAAATA
184375 T-AAA-TTAT-TAATATA
1 TAAAATTTATATAA-ATA
184390 TCAAAATTTATATAAATA
1 T-AAAATTTATATAAATA
184408 TAAAATATT-T-TAAATA
1 TAAAAT-TTATATAAATA
184424 TAA
1 TAA
184427 TTATAATATT
Statistics
Matches: 44, Mismatches: 1, Indels: 14
0.75 0.02 0.24
Matches are distributed among these distances:
13 1 0.02
14 4 0.09
15 7 0.16
16 10 0.23
17 9 0.20
18 10 0.23
19 3 0.07
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAAATTTATATAAATA
Found at i:184452 original size:18 final size:18
Alignment explanation
Indices: 184387--184453 Score: 66
Period size: 18 Copynumber: 3.7 Consensus size: 18
184377 AATTATTAAT
*
184387 ATATCAAAAT-TTATATAA
1 ATATTAAAATATTATA-AA
*
184405 ATA-TAAAATATTTTAAA
1 ATATTAAAATATTATAAA
*
184422 TATAATTATAATATTATAAA
1 -AT-ATTAAAATATTATAAA
184442 ATATTAAAATAT
1 ATATTAAAATAT
184454 AATATTAAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
17 7 0.17
18 18 0.45
19 3 0.08
20 12 0.30
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (18 bp):
ATATTAAAATATTATAAA
Found at i:185084 original size:22 final size:23
Alignment explanation
Indices: 185050--185093 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
185040 TAGATATCTA
* *
185050 AAATAGTATATATTAAA-ATTTT
1 AAATAATAAATATTAAATATTTT
185072 AAATAATAAATATTAAATATTT
1 AAATAATAAATATTAAATATTT
185094 ATTAAAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (23 bp):
AAATAATAAATATTAAATATTTT
Found at i:185271 original size:18 final size:18
Alignment explanation
Indices: 185248--185287 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
185238 CATTACTTTA
185248 ATAATTTATTTT-AATATC
1 ATAA-TTATTTTCAATATC
*
185266 ATAATTATTTTCAATCTC
1 ATAATTATTTTCAATATC
185284 ATAA
1 ATAA
185288 AAATCATTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (18 bp):
ATAATTATTTTCAATATC
Found at i:185580 original size:9 final size:9
Alignment explanation
Indices: 185566--185599 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
185556 AGGAATTTAA
185566 TTTTTAAAT
1 TTTTTAAAT
185575 TTTTTAAAT
1 TTTTTAAAT
*
185584 TTATTAAAT
1 TTTTTAAAT
185593 ATTTTTA
1 -TTTTTA
185600 TTTAAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 17 0.77
10 5 0.23
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (9 bp):
TTTTTAAAT
Found at i:185592 original size:18 final size:18
Alignment explanation
Indices: 185564--185599 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
185554 ATAGGAATTT
185564 AATTTTTAAAT-TTTTTA
1 AATTTTTAAATATTTTTA
185581 AATTTATTAAATATTTTTA
1 AATTT-TTAAATATTTTTA
185600 TTTAAAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
18 6 0.35
19 6 0.35
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
AATTTTTAAATATTTTTA
Found at i:188886 original size:42 final size:41
Alignment explanation
Indices: 188839--188918 Score: 133
Period size: 42 Copynumber: 1.9 Consensus size: 41
188829 AAATAAGTGT
*
188839 GAATATTGTTATCTCAGAGAGATCTGATTTTTTATTTTCTAC
1 GAATATTGCTATCTCAGAGAGATCTGA-TTTTTATTTTCTAC
*
188881 GAATATTGCTATCTCAGAGGGATCTGATTTTTATTTTC
1 GAATATTGCTATCTCAGAGAGATCTGATTTTTATTTTC
188919 ATGATTCCTT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
41 11 0.31
42 25 0.69
ACGTcount: A:0.25, C:0.12, G:0.16, T:0.46
Consensus pattern (41 bp):
GAATATTGCTATCTCAGAGAGATCTGATTTTTATTTTCTAC
Found at i:189374 original size:29 final size:30
Alignment explanation
Indices: 189341--189452 Score: 93
Period size: 31 Copynumber: 3.6 Consensus size: 30
189331 TTTTTATTTT
*
189341 TTTAAATATAA-ATAATATTTTAATAATTA
1 TTTAAATATAATATAATATTTTAATTATTA
* * *
189370 TTTAATATAAAATATAATTTTATTAATTTATTT
1 TTTAA-ATATAATATAATATT-TTAA-TTATTA
* *
189403 TTAATAAATATAATTTAATATTTTTTATTATTA
1 TT--TAAATATAATATAATA-TTTTAATTATTA
189436 TTT-AATATAAATATAAT
1 TTTAAATAT-AATATAAT
189453 TTCAATTATT
Statistics
Matches: 65, Mismatches: 10, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
29 5 0.08
30 10 0.15
31 15 0.23
32 4 0.06
33 13 0.20
34 13 0.20
35 5 0.08
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (30 bp):
TTTAAATATAATATAATATTTTAATTATTA
Found at i:189410 original size:30 final size:34
Alignment explanation
Indices: 189344--189454 Score: 92
Period size: 29 Copynumber: 3.3 Consensus size: 34
189334 TTATTTTTTT
* *
189344 AAATATAAATAATATTTTAATA--ATTATTTAATATA
1 AAATATAATTTATA-TTTAATATTATTATTT-A-ATA
189379 AAATATAATTT-TA-TTAAT-TTATT-TTTAAT-
1 AAATATAATTTATATTTAATATTATTATTTAATA
**
189408 AAATATAATTTAATATTTTTTATTATTATTTAATA
1 AAATATAATTT-ATATTTAATATTATTATTTAATA
189443 TAAATATAATTT
1 -AAATATAATTT
189455 CAATTATTTA
Statistics
Matches: 63, Mismatches: 4, Indels: 17
0.75 0.05 0.20
Matches are distributed among these distances:
29 11 0.17
30 2 0.03
31 3 0.05
32 11 0.17
33 8 0.13
34 8 0.13
35 9 0.14
36 11 0.17
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (34 bp):
AAATATAATTTATATTTAATATTATTATTTAATA
Found at i:189426 original size:36 final size:39
Alignment explanation
Indices: 189386--189467 Score: 97
Period size: 36 Copynumber: 2.2 Consensus size: 39
189376 ATAAAATATA
189386 ATTTTATTAATTTATT-TTT-A-ATAAATATAATTT-AAT
1 ATTTTATTAA-TTATTATTTAATATAAATATAATTTCAAT
189422 ATTTT-TT-ATTATTATTTAATATAAATATAATTTCAAT
1 ATTTTATTAATTATTATTTAATATAAATATAATTTCAAT
189459 -TATTTATTA
1 AT-TTTATTA
189468 TATAAATACA
Statistics
Matches: 39, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
33 5 0.13
34 4 0.10
35 3 0.08
36 19 0.49
37 6 0.15
38 2 0.05
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (39 bp):
ATTTTATTAATTATTATTTAATATAAATATAATTTCAAT
Found at i:189464 original size:65 final size:63
Alignment explanation
Indices: 189333--189501 Score: 182
Period size: 65 Copynumber: 2.6 Consensus size: 63
189323 AGCCCTCTTT
* *
189333 TTTATTTTTTTAAATATAAATAATATTTTAATAATTATTTAATATAAAATATAATTTTATTAA
1 TTTATTTTTATAAATATAAATAATATTTTAATAATTATTTAATATAAAATATAATTTAATTAA
* * *
189396 TTTATTTTTAATAAATATAATTTAATATTTTTTATTATTATTTAATAT-AAATATAATTTCAATT
1 TTTATTTTT-ATAAATATAA-ATAATA-TTTTAATAATTATTTAATATAAAATATAATTT-AATT
189460 -A
62 AA
* *
189461 TTTA-TTATATAAATACACAATTAAATATTTTTAATAATTAT
1 TTTATTTTTATAAATATA-AA-T-AATA-TTTTAATAATTAT
189502 ATTTTATTTA
Statistics
Matches: 89, Mismatches: 10, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
63 17 0.19
64 14 0.16
65 37 0.42
66 21 0.24
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (63 bp):
TTTATTTTTATAAATATAAATAATATTTTAATAATTATTTAATATAAAATATAATTTAATTAA
Found at i:189574 original size:21 final size:21
Alignment explanation
Indices: 189550--189601 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
189540 ACATATATTC
*
189550 TATTACTAAT-TTTAACTTAAT
1 TATTA-TAATATTTAAATTAAT
*
189571 TATTATAATATTTAAATTTAT
1 TATTATAATATTTAAATTAAT
*
189592 TATTTTAATA
1 TATTATAATA
189602 ACTGATCTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 4 0.15
21 23 0.85
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (21 bp):
TATTATAATATTTAAATTAAT
Found at i:191974 original size:27 final size:28
Alignment explanation
Indices: 191913--191979 Score: 70
Period size: 27 Copynumber: 2.5 Consensus size: 28
191903 TATTTTTTAA
191913 AATTT-AAATAATATTTTTTAAAAATTT
1 AATTTAAAATAATATTTTTTAAAAATTT
* * *
191940 GATATAAAAT-ATATTTATTTATAAA-TT
1 AATTTAAAATAATATTT-TTTAAAAATTT
191967 AATTTAAAA-AATA
1 AATTTAAAATAATA
191980 AATATATTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
27 21 0.66
28 11 0.34
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.46
Consensus pattern (28 bp):
AATTTAAAATAATATTTTTTAAAAATTT
Found at i:192088 original size:16 final size:15
Alignment explanation
Indices: 192058--192091 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
192048 AAAGTTATTT
*
192058 TTAATTATTATTAAA
1 TTAATTATAATTAAA
192073 TTAATATATAATTAAA
1 TTAAT-TATAATTAAA
192089 TTA
1 TTA
192092 TATTCTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TTAATTATAATTAAA
Found at i:192751 original size:7 final size:7
Alignment explanation
Indices: 192739--192763 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
192729 TAATAAAAAG
192739 TTAATAA
1 TTAATAA
192746 TTAATAA
1 TTAATAA
192753 TTAATAA
1 TTAATAA
192760 TTAA
1 TTAA
192764 CTAAAATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
TTAATAA
Found at i:199417 original size:18 final size:18
Alignment explanation
Indices: 199390--199424 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
199380 TATAATTATT
199390 TTTAAAAAATATAAAATA
1 TTTAAAAAATATAAAATA
*
199408 TTTAATAAATATAAAAT
1 TTTAAAAAATATAAAAT
199425 TTGAATCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
TTTAAAAAATATAAAATA
Found at i:200492 original size:9 final size:10
Alignment explanation
Indices: 200467--200497 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
200457 AAAGGGAGGG
200467 AGAAAAAGAA
1 AGAAAAAGAA
200477 AGAAAAAGAA
1 AGAAAAAGAA
*
200487 GGAAAAAGAA
1 AGAAAAAGAA
200497 A
1 A
200498 ATGGAAACGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (10 bp):
AGAAAAAGAA
Found at i:203444 original size:35 final size:34
Alignment explanation
Indices: 203405--203472 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 34
203395 AAAATTTTGT
*
203405 TAATTGAATGATTAAAATTAATAACTATTTTTTTA
1 TAATTGAATGATT-AAATTAACAACTATTTTTTTA
* * * *
203440 TAATTTATTTATTAAATTAACAAGTATTTTTTT
1 TAATTGAATGATTAAATTAACAACTATTTTTTT
203473 CATTTTCGAT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
34 18 0.64
35 10 0.36
ACGTcount: A:0.40, C:0.03, G:0.04, T:0.53
Consensus pattern (34 bp):
TAATTGAATGATTAAATTAACAACTATTTTTTTA
Found at i:203932 original size:2 final size:2
Alignment explanation
Indices: 203925--203949 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
203915 GTTAGGCTAT
203925 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 T
203950 TTTTGGACAC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:204302 original size:17 final size:17
Alignment explanation
Indices: 204280--204316 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
204270 AAAGTAAATC
**
204280 AAATATTTATTTTTTTT
1 AAATATTTAAATTTTTT
204297 AAATATTTAAATTTTTT
1 AAATATTTAAATTTTTT
204314 AAA
1 AAA
204317 ATAAAAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
AAATATTTAAATTTTTT
Found at i:204313 original size:18 final size:17
Alignment explanation
Indices: 204280--204319 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
204270 AAAGTAAATC
* *
204280 AAATATTTATTTTTTTT
1 AAATATTTAATTTTTTA
204297 AAATATTTAAATTTTTTA
1 AAATATTT-AATTTTTTA
204315 AAATA
1 AAATA
204320 AAAATATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
AAATATTTAATTTTTTA
Found at i:205157 original size:31 final size:32
Alignment explanation
Indices: 205101--205161 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
205091 TACTTTCTTT
205101 TTCAGAAGATTATGAGATTTTTTTTCATCCAC
1 TTCAGAAGATTATGAGATTTTTTTTCATCCAC
205133 TTCAGAAGATTATGAGA-TTTTTTTCATCC
1 TTCAGAAGATTATGAGATTTTTTTTCATCC
205162 CCCAAGCCTG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 12 0.41
32 17 0.59
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.44
Consensus pattern (32 bp):
TTCAGAAGATTATGAGATTTTTTTTCATCCAC
Found at i:205519 original size:2 final size:2
Alignment explanation
Indices: 205512--205542 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
205502 TTTCATACGA
205512 AT 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 AT A
205543 AGCCTTCTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:210484 original size:2 final size:2
Alignment explanation
Indices: 210472--210505 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
210462 AAAGATATGA
* *
210472 AT AT TT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
210506 CTGGTCTCCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
AT
Found at i:212318 original size:2 final size:2
Alignment explanation
Indices: 212313--212345 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
212303 CATGTGTGTG
*
212313 TA TA TA TA TA TA TA TA TA TA AA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
212346 AATGCAAAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:212859 original size:16 final size:16
Alignment explanation
Indices: 212829--212870 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
212819 CGCCTTGTTA
212829 AAAAGAAAAAAAAAAGG
1 AAAAG-AAAAAAAAAGG
*
212846 AAAAGAAAACAAAAGG
1 AAAAGAAAAAAAAAGG
*
212862 AAAGGAAAA
1 AAAAGAAAA
212871 TATAGAACTG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 18 0.78
17 5 0.22
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (16 bp):
AAAAGAAAAAAAAAGG
Found at i:214856 original size:6 final size:6
Alignment explanation
Indices: 214840--214884 Score: 56
Period size: 6 Copynumber: 7.5 Consensus size: 6
214830 TGCAAAACAC
* *
214840 AGAAAA A-AAAA AGAAAA AGAAAA TGAAAA AAAAAA AGAGAAA AGA
1 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGA-AAA AGA
214885 TATGAGATGA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
5 5 0.15
6 22 0.67
7 6 0.18
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (6 bp):
AGAAAA
Found at i:214868 original size:20 final size:20
Alignment explanation
Indices: 214844--214882 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
214834 AAACACAGAA
*
214844 AAAAAAAAGAAAAAGAAAATG
1 AAAAAAAA-AAAGAGAAAATG
214865 AAAAAAAAAAAGAGAAAA
1 AAAAAAAAAAAGAGAAAA
214883 GATATGAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.85, C:0.00, G:0.13, T:0.03
Consensus pattern (20 bp):
AAAAAAAAAAAGAGAAAATG
Found at i:215071 original size:20 final size:20
Alignment explanation
Indices: 215046--215087 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
215036 ACCTCTGAGG
**
215046 AAATTAAAAAATTAAAAAAA
1 AAATTAAAAAACCAAAAAAA
*
215066 AAATTAAAGAACCAAAAAAA
1 AAATTAAAAAACCAAAAAAA
215086 AA
1 AA
215088 GGTATTCACG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.79, C:0.05, G:0.02, T:0.14
Consensus pattern (20 bp):
AAATTAAAAAACCAAAAAAA
Found at i:215278 original size:21 final size:21
Alignment explanation
Indices: 215232--215280 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
215222 CGCCAAAAAA
**
215232 GCACACATGCACACGTGCGTG
1 GCACACATGCACAAATGCGTG
*
215253 CCACACATGC-CAAATGCGTG
1 GCACACATGCACAAATGCGTG
215273 TGCACACA
1 -GCACACA
215281 AACCACTCGA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.29, C:0.35, G:0.22, T:0.14
Consensus pattern (21 bp):
GCACACATGCACAAATGCGTG
Found at i:216842 original size:2 final size:2
Alignment explanation
Indices: 216829--216860 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
216819 CTCTACCTGC
*
216829 AT AT AC 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
216861 GCAGCATTTT
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:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:217531 original size:2 final size:2
Alignment explanation
Indices: 217524--217563 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
217514 TACTATCTTT
217524 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
217564 CGAAGAATGC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:219509 original size:31 final size:32
Alignment explanation
Indices: 219452--219511 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
219442 AAAATAGTAA
* *
219452 TAAATTAAAATTAATTTTATAATTATTTATAT
1 TAAATTAAAATAAAATTTATAATTATTTATAT
219484 TAAATTAAAATAAAATTT-TAATTATTTA
1 TAAATTAAAATAAAATTTATAATTATTTA
219512 AATAATAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 10 0.38
32 16 0.62
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (32 bp):
TAAATTAAAATAAAATTTATAATTATTTATAT
Found at i:220286 original size:31 final size:31
Alignment explanation
Indices: 220220--220292 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 31
220210 TTAATAATAT
* *
220220 TATAAATAATAAATTAATTAGTTAATTAAAC
1 TATAAAAAATAAATTAATAAGTTAATTAAAC
*
220251 TATAAAAAATAAATT-ATAATTTAACTT-AAC
1 TATAAAAAATAAATTAATAAGTTAA-TTAAAC
220281 ATATAAATAAAT
1 -TATAAA-AAAT
220293 TTACTTAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
30 10 0.28
31 22 0.61
32 4 0.11
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.37
Consensus pattern (31 bp):
TATAAAAAATAAATTAATAAGTTAATTAAAC
Found at i:221774 original size:19 final size:22
Alignment explanation
Indices: 221742--221789 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
221732 ATCAAAAGTC
221742 ATATTATTTAATTAAATA-TA-T
1 ATATT-TTTAATTAAATATTATT
221763 ATATTTTT-ATTAAATATTATT
1 ATATTTTTAATTAAATATTATT
221784 ATATTT
1 ATATTT
221790 AATATTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 8 0.32
20 5 0.20
21 12 0.48
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
ATATTTTTAATTAAATATTATT
Found at i:221790 original size:19 final size:19
Alignment explanation
Indices: 221742--221790 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
221732 ATCAAAAGTC
221742 ATAT-TATTTAATTAAATAT
1 ATATATATTT-ATTAAATAT
*
221761 ATATATTTTTATTAAATAT
1 ATATATATTTATTAAATAT
221780 -TATTATATTTA
1 ATA-TATATTTA
221791 ATATTAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 2 0.08
19 20 0.77
20 4 0.15
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
ATATATATTTATTAAATAT
Found at i:222380 original size:48 final size:49
Alignment explanation
Indices: 222280--222372 Score: 120
Period size: 47 Copynumber: 1.9 Consensus size: 49
222270 TCCGCAGCTT
* *
222280 AAAATAATAATATATATTAAAATTTTAAATTTATTAAATATTAATTGTTA
1 AAAATAATAATATAAATT-AAATTTTAAATTTATTAAATAATAATTGTTA
*
222330 AAAATAATTATATAAATT-AA-TTTAAATTT-TTAATATAATAATT
1 AAAATAATAATATAAATTAAATTTTAAATTTATTAA-ATAATAATT
222373 TTTTAAAAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
46 4 0.10
47 17 0.44
48 2 0.05
50 16 0.41
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (49 bp):
AAAATAATAATATAAATTAAATTTTAAATTTATTAAATAATAATTGTTA
Found at i:223252 original size:17 final size:19
Alignment explanation
Indices: 223224--223258 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
223214 TATTTTTTTA
223224 TATTTCTATCAA-TAAAAC
1 TATTTCTATCAATTAAAAC
223242 TATTT-TATCAATTAAAA
1 TATTTCTATCAATTAAAA
223259 ATAAATTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (19 bp):
TATTTCTATCAATTAAAAC
Found at i:224250 original size:2 final size:2
Alignment explanation
Indices: 224243--224272 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
224233 CTAGGAAAAC
224243 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
224273 CATTGTTTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:227224 original size:2 final size:2
Alignment explanation
Indices: 227217--227253 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
227207 ATTGAAAGAA
227217 AT AT AT AT 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 AT AT AT AT A
227254 AAAGAGATTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:228832 original size:3 final size:3
Alignment explanation
Indices: 228824--228853 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
228814 GCTAAAAGTT
228824 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
228854 CATTAAAAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:230373 original size:13 final size:13
Alignment explanation
Indices: 230357--230381 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
230347 ATATTACTAA
230357 TAAAAAAATTTAT
1 TAAAAAAATTTAT
230370 TAAAAAAATTTA
1 TAAAAAAATTTA
230382 AAATATAGTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
TAAAAAAATTTAT
Found at i:233440 original size:2 final size:2
Alignment explanation
Indices: 233433--233475 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
233423 ACTTTTTAAC
233433 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
233475 T
1 T
233476 CAGATTCGTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:236453 original size:20 final size:21
Alignment explanation
Indices: 236404--236453 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
236394 GATAAAAATC
* *
236404 AAATATCTAAAATGATATATT
1 AAATATATAAAATGAAATATT
*
236425 AAATCTATAAAAT-AAATATT
1 AAATATATAAAATGAAATATT
*
236445 ACATATATA
1 AAATATATA
236454 TAGCATAAAG
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 13 0.54
21 11 0.46
ACGTcount: A:0.56, C:0.06, G:0.02, T:0.36
Consensus pattern (21 bp):
AAATATATAAAATGAAATATT
Found at i:236782 original size:44 final size:44
Alignment explanation
Indices: 236693--236801 Score: 119
Period size: 44 Copynumber: 2.5 Consensus size: 44
236683 ATCTTTGAAG
* * *
236693 AATCATATCTTATAATTTAGGTTAGAAGTCAAATAGAGCTATAT
1 AATCATATCTTATAATTTAGGTTAAAAATCAAATACAGCTATAT
* * * * * *
236737 AATCAGATCCTATAATTTAGGTTAAAAATTAACTACAGTTGTAT
1 AATCATATCTTATAATTTAGGTTAAAAATCAAATACAGCTATAT
* *
236781 AATTATATCTTACAATTTAGG
1 AATCATATCTTATAATTTAGG
236802 CTATTAATTA
Statistics
Matches: 52, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
44 52 1.00
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (44 bp):
AATCATATCTTATAATTTAGGTTAAAAATCAAATACAGCTATAT
Found at i:236940 original size:37 final size:37
Alignment explanation
Indices: 236890--236962 Score: 119
Period size: 37 Copynumber: 2.0 Consensus size: 37
236880 AAAAATTCTG
236890 ATCATTTTTCATCAATTCTAATTTTTCTTTCTTTATA
1 ATCATTTTTCATCAATTCTAATTTTTCTTTCTTTATA
* * *
236927 ATCATTTTTCATCAGTTCTGATTTTTTTTTCTTTAT
1 ATCATTTTTCATCAATTCTAATTTTTCTTTCTTTAT
236963 GGTATCAGAG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.21, C:0.15, G:0.03, T:0.62
Consensus pattern (37 bp):
ATCATTTTTCATCAATTCTAATTTTTCTTTCTTTATA
Found at i:237125 original size:46 final size:44
Alignment explanation
Indices: 237019--237151 Score: 160
Period size: 45 Copynumber: 3.0 Consensus size: 44
237009 AACACCTTCC
* * * *
237019 CAGAATCTGTTCTATTCAGCTTTCATTGCTGGAATTTTTTCTTTT
1 CAGAATCTGTTTTATTTAGCCTTCATTGCTGAAATTTTTT-TTTT
* *
237064 CAAAATCTGTATTATTTAGCCTTCATTGCTGAAATTTTTTTATTT
1 CAGAATCTGTTTTATTTAGCCTTCATTGCTGAAATTTTTTT-TTT
*
237109 GCAGAATCTGTTTTATTTAGCCTTCATTG-TTATAATTTTTTTT
1 -CAGAATCTGTTTTATTTAGCCTTCATTGCTGA-AATTTTTTTT
237152 CTCTACTTTC
Statistics
Matches: 76, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
44 1 0.01
45 40 0.53
46 35 0.46
ACGTcount: A:0.22, C:0.14, G:0.11, T:0.53
Consensus pattern (44 bp):
CAGAATCTGTTTTATTTAGCCTTCATTGCTGAAATTTTTTTTTT
Found at i:240701 original size:21 final size:21
Alignment explanation
Indices: 240675--240714 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
240665 CACAGCTTTA
*
240675 ATTGT-ATATGTAGATGATATC
1 ATTGTAATA-GTAAATGATATC
240696 ATTGTAATAGTAAATGATA
1 ATTGTAATAGTAAATGATA
240715 AGAGAGAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.40, C:0.03, G:0.17, T:0.40
Consensus pattern (21 bp):
ATTGTAATAGTAAATGATATC
Found at i:241754 original size:44 final size:44
Alignment explanation
Indices: 241681--241792 Score: 143
Period size: 44 Copynumber: 2.5 Consensus size: 44
241671 TACATTGAAA
* *
241681 AATCAGATCCTACAATTTAAGCTAGAAGTCAAATACAACTATAT
1 AATCAGATCCTACAATTTAGGCTAAAAGTCAAATACAACTATAT
* * * ** *
241725 AATCAGATCTTACTATTTAGGCTAAAAGTCAATTACAGTTGTAT
1 AATCAGATCCTACAATTTAGGCTAAAAGTCAAATACAACTATAT
*
241769 AATCATATCCTACAATTTAGGCTA
1 AATCAGATCCTACAATTTAGGCTA
241793 TTAATTAGGA
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
44 57 1.00
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.32
Consensus pattern (44 bp):
AATCAGATCCTACAATTTAGGCTAAAAGTCAAATACAACTATAT
Found at i:250305 original size:27 final size:27
Alignment explanation
Indices: 250275--250334 Score: 88
Period size: 27 Copynumber: 2.2 Consensus size: 27
250265 TATATGCGTG
250275 TTATATTT-AAATATTTT-TATATTATAA
1 TTATATTTAAAATATTTTATAT-TTAT-A
250302 TTATATTTAAAATATTTTATATTTATA
1 TTATATTTAAAATATTTTATATTTATA
250329 TTATAT
1 TTATAT
250335 AAATTTTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
27 15 0.48
28 13 0.42
29 3 0.10
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (27 bp):
TTATATTTAAAATATTTTATATTTATA
Found at i:250368 original size:16 final size:15
Alignment explanation
Indices: 250275--250401 Score: 84
Period size: 15 Copynumber: 8.4 Consensus size: 15
250265 TATATGCGTG
* *
250275 TTATATTTAAATATTT
1 TTATA-TTATATATAT
250291 TTATATTATAATTATAT
1 TTATATTAT-A-TATAT
* * *
250308 TTAAAATATTTTATAT
1 TTATATTA-TATATAT
*
250324 TTATATTATATAAAT
1 TTATATTATATATAT
**
250339 TT-TAAAATATATAT
1 TTATATTATATATAT
250353 TTATATTATATCATA-
1 TTATATTATAT-ATAT
*
250368 TTATATT-TTTATTAT
1 TTATATTATATA-TAT
250383 TT-TA-TATATATAT
1 TTATATTATATATAT
250396 TTATAT
1 TTATAT
250402 AACCATATCT
Statistics
Matches: 85, Mismatches: 16, Indels: 21
0.70 0.13 0.17
Matches are distributed among these distances:
13 7 0.08
14 22 0.26
15 25 0.29
16 20 0.24
17 10 0.12
18 1 0.01
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (15 bp):
TTATATTATATATAT
Found at i:250374 original size:21 final size:22
Alignment explanation
Indices: 250345--250401 Score: 80
Period size: 21 Copynumber: 2.6 Consensus size: 22
250335 AAATTTTAAA
250345 ATATATATTTATATTATATCAT
1 ATATATATTTATATTATATCAT
* * *
250367 AT-TATATTTTTATTATTTTAT
1 ATATATATTTATATTATATCAT
250388 ATATATATTTATAT
1 ATATATATTTATAT
250402 AACCATATCT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 18 0.60
22 12 0.40
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (22 bp):
ATATATATTTATATTATATCAT
Found at i:251874 original size:14 final size:14
Alignment explanation
Indices: 251857--251908 Score: 68
Period size: 15 Copynumber: 3.6 Consensus size: 14
251847 TTATTTCAAT
251857 AATTAACAATAAAA
1 AATTAACAATAAAA
*
251871 AATTAATTAATAAAA
1 AATTAA-CAATAAAA
*
251886 ACATTAAAAATAAAA
1 A-ATTAACAATAAAA
251901 AATTAACA
1 AATTAACA
251909 TAGAATAGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
14 12 0.36
15 16 0.48
16 5 0.15
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (14 bp):
AATTAACAATAAAA
Found at i:252006 original size:8 final size:8
Alignment explanation
Indices: 251993--252038 Score: 76
Period size: 8 Copynumber: 5.8 Consensus size: 8
251983 TTAAAATTTC
251993 TATTTTAA
1 TATTTTAA
252001 TATTTTTAA
1 TA-TTTTAA
252010 TATTTTAA
1 TATTTTAA
252018 TATTTTAA
1 TATTTTAA
252026 T-TTTTAA
1 TATTTTAA
252033 TATTTT
1 TATTTT
252039 TATAAATTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
7 7 0.19
8 21 0.58
9 8 0.22
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (8 bp):
TATTTTAA
Found at i:252009 original size:9 final size:9
Alignment explanation
Indices: 251995--252040 Score: 64
Period size: 9 Copynumber: 5.6 Consensus size: 9
251985 AAAATTTCTA
251995 TTTTAATAT
1 TTTTAATAT
252004 TTTTAATA-
1 TTTTAATAT
252012 TTTTAATA-
1 TTTTAATAT
252020 TTTT-A-AT
1 TTTTAATAT
252027 TTTTAATAT
1 TTTTAATAT
252036 TTTTA
1 TTTTA
252041 TAAATTAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
6 1 0.03
7 5 0.15
8 13 0.38
9 15 0.44
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (9 bp):
TTTTAATAT
Found at i:252048 original size:23 final size:23
Alignment explanation
Indices: 252002--252051 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
251992 CTATTTTAAT
**
252002 ATTTTTAATATTTTAATATTTTA
1 ATTTTTAATATTTTAATAAATTA
*
252025 ATTTTTAATATTTTTATAAATTA
1 ATTTTTAATATTTTAATAAATTA
252048 ATTT
1 ATTT
252052 GTTGTTGTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (23 bp):
ATTTTTAATATTTTAATAAATTA
Found at i:252049 original size:31 final size:31
Alignment explanation
Indices: 251979--252049 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
251969 CTTTCATTTC
*
251979 TAAATTAAAATTTCTATTTTAATATTTTTAA
1 TAAATTAATATTTCTATTTTAATATTTTTAA
**
252010 TATTTTAATATTT-TAATTTTTAATATTTTT-A
1 TAAATTAATATTTCT-A-TTTTAATATTTTTAA
252041 TAAATTAAT
1 TAAATTAAT
252050 TTGTTGTTGT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
30 1 0.03
31 19 0.58
32 13 0.39
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.59
Consensus pattern (31 bp):
TAAATTAATATTTCTATTTTAATATTTTTAA
Found at i:257546 original size:37 final size:38
Alignment explanation
Indices: 257460--257546 Score: 101
Period size: 37 Copynumber: 2.3 Consensus size: 38
257450 TTTAATTTAA
* *
257460 TTAATCTATTT-TTTAATATAAAATAATTTTGATAGCTT
1 TTAAT-TATTTATTTAATATAAAATAATTTTAATAGATT
257498 TTAATTA-TTATTTAATATAAATATAA-TTTAATA-ATT
1 TTAATTATTTATTTAATATAAA-ATAATTTTAATAGATT
*
257534 TTGATTATTTATT
1 TTAATTATTTATT
257547 ATAGATACAT
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
36 10 0.23
37 24 0.56
38 9 0.21
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.55
Consensus pattern (38 bp):
TTAATTATTTATTTAATATAAAATAATTTTAATAGATT
Found at i:263870 original size:18 final size:18
Alignment explanation
Indices: 263847--263885 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
263837 AAAGGCGAGT
263847 AGATGAAGAT-ACAGAAGA
1 AGATGAAGATGA-AGAAGA
263865 AGATGAAGATGAAGAAGA
1 AGATGAAGATGAAGAAGA
263883 AGA
1 AGA
263886 GTTAGCGAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 19 0.95
19 1 0.05
ACGTcount: A:0.56, C:0.03, G:0.31, T:0.10
Consensus pattern (18 bp):
AGATGAAGATGAAGAAGA
Found at i:263945 original size:25 final size:25
Alignment explanation
Indices: 263895--263945 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
263885 AGTTAGCGAG
* * *
263895 GAAGGAAAGGAGGGGAGTGGGGGAA
1 GAAGGAAAGGAAGGAAGTGAGGGAA
*
263920 GAAGGAAAGGAAGGAAGTGAGTGAA
1 GAAGGAAAGGAAGGAAGTGAGGGAA
263945 G
1 G
263946 CGTGGAAGGG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.53, T:0.06
Consensus pattern (25 bp):
GAAGGAAAGGAAGGAAGTGAGGGAA
Found at i:275282 original size:10 final size:10
Alignment explanation
Indices: 275267--275294 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
275257 AAGGTTGGCC
275267 AAAGAAAAAA
1 AAAGAAAAAA
275277 AAAGAAAAAA
1 AAAGAAAAAA
275287 AAAGAAAA
1 AAAGAAAA
275295 TAAGAGCTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (10 bp):
AAAGAAAAAA
Found at i:278682 original size:14 final size:14
Alignment explanation
Indices: 278665--278698 Score: 52
Period size: 13 Copynumber: 2.4 Consensus size: 14
278655 AATTAAAAAT
278665 AAAAATTTTA-TAA
1 AAAAATTTTATTAA
278678 AAAAATTTTATTAA
1 AAAAATTTTATTAA
278692 ACAAAAT
1 A-AAAAT
278699 AAAATGATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 10 0.53
14 4 0.21
15 5 0.26
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (14 bp):
AAAAATTTTATTAA
Found at i:279303 original size:3 final size:3
Alignment explanation
Indices: 279295--279324 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
279285 TAATTTTAAC
*
279295 TTA TTA TTA TTA TTA TTA TTA TTA TAA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
279325 AAGTTCAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:286465 original size:11 final size:13
Alignment explanation
Indices: 286435--286464 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
286425 TTGAATTATA
286435 AAAAAATAATATT
1 AAAAAATAATATT
286448 AAAAAATAATA-T
1 AAAAAATAATATT
286460 AAAAA
1 AAAAA
286465 TTGTAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
AAAAAATAATATT
Found at i:287808 original size:13 final size:13
Alignment explanation
Indices: 287792--287841 Score: 50
Period size: 13 Copynumber: 3.9 Consensus size: 13
287782 TCTAAATTAA
287792 ATTATAAAATATT
1 ATTATAAAATATT
* *
287805 ATTATAACATATC
1 ATTATAAAATATT
287818 A-TAT-AAATCATT
1 ATTATAAAAT-ATT
*
287830 ATAATAAAATAT
1 ATTATAAAATAT
287842 ATGTACTATT
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
11 3 0.10
12 6 0.21
13 16 0.55
14 4 0.14
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (13 bp):
ATTATAAAATATT
Found at i:288913 original size:30 final size:30
Alignment explanation
Indices: 288839--288914 Score: 93
Period size: 30 Copynumber: 2.5 Consensus size: 30
288829 ATATTAAACG
*
288839 TTAAGAGTTTATTTAAACAAAAACTAAAAA
1 TTAAGAGTTTATTTGAACAAAAACTAAAAA
*
288869 TTAAG-GATTTATTTGAATATAAAA-TAAAAA
1 TTAAGAG-TTTATTTGAACA-AAAACTAAAAA
*
288899 TTAAGAGTTGATTTGA
1 TTAAGAGTTTATTTGA
288915 GTGTAATAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
29 1 0.03
30 34 0.85
31 5 0.12
ACGTcount: A:0.50, C:0.03, G:0.12, T:0.36
Consensus pattern (30 bp):
TTAAGAGTTTATTTGAACAAAAACTAAAAA
Found at i:290463 original size:17 final size:18
Alignment explanation
Indices: 290443--290476 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
290433 TTCTACATGA
290443 TTATAATA-TAAAATATT
1 TTATAATATTAAAATATT
*
290460 TTATTATATTAAAATAT
1 TTATAATATTAAAATAT
290477 ATAAAATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTATAATATTAAAATATT
Found at i:290798 original size:21 final size:21
Alignment explanation
Indices: 290780--290820 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
290770 AAAAATAACT
290780 AAAATA-TAATATAATATAAA
1 AAAATATTAATATAATATAAA
290800 AAAATATTAATATAATATAAA
1 AAAATATTAATATAATATAAA
290821 TGTAAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (21 bp):
AAAATATTAATATAATATAAA
Found at i:290827 original size:26 final size:27
Alignment explanation
Indices: 290782--290833 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
290772 AAATAACTAA
290782 AATATAATATAATATAAAAAA-ATATT
1 AATATAATATAATATAAAAAATATATT
*
290808 AATATAATATAA-ATGTAAAAATATAT
1 AATATAATATAATAT-AAAAAATATAT
290834 CAACATTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 2 0.09
26 17 0.74
27 4 0.17
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (27 bp):
AATATAATATAATATAAAAAATATATT
Found at i:291069 original size:14 final size:14
Alignment explanation
Indices: 291050--291109 Score: 57
Period size: 15 Copynumber: 3.9 Consensus size: 14
291040 AAATTTATAT
291050 AAAAATAATTAATA
1 AAAAATAATTAATA
291064 AAAAATAATATAATA
1 AAAAATAAT-TAATA
* *
291079 TAAAATTTATTAATTA
1 -AAAAATAATTAA-TA
291095 AAATTAATAATTAAT
1 AAA--AATAATTAAT
291110 GTTCTTAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
14 9 0.24
15 11 0.30
16 10 0.27
17 7 0.19
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
AAAAATAATTAATA
Found at i:291081 original size:30 final size:30
Alignment explanation
Indices: 291046--291103 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
291036 ATTAAAATTT
291046 ATATAAAAATAATTAATAAAAAATAATATA
1 ATATAAAAATAATTAATAAAAAATAATATA
* * * *
291076 ATATAAAATTTATTAATTAAAATTAATA
1 ATATAAAAATAATTAATAAAAAATAATA
291104 ATTAATGTTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (30 bp):
ATATAAAAATAATTAATAAAAAATAATATA
Found at i:297793 original size:2 final size:2
Alignment explanation
Indices: 297786--297817 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
297776 TGAAGCTCTG
297786 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
297818 ACAAGAAGGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:298554 original size:21 final size:21
Alignment explanation
Indices: 298521--298562 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
298511 TTTGAAGTTG
298521 ATTATTTAATAA-TTTATTTT
1 ATTATTTAATAATTTTATTTT
298541 ATTATTTAAATAATTTTATTTT
1 ATTATTT-AATAATTTTATTTT
298563 TATATTAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 7 0.35
21 5 0.25
22 8 0.40
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
ATTATTTAATAATTTTATTTT
Done.