Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold522
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: 216214
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
File 2 of 2
Found at i:143046 original size:39 final size:39
Alignment explanation
Indices: 142974--143053 Score: 97
Period size: 39 Copynumber: 2.1 Consensus size: 39
142964 AACCAATCCT
* * * * * *
142974 TTCAGTCCCGCTAAGCATTCTGTTTAATTTTCCACTTTG
1 TTCAATCCCACTAAACATTCTGGTAAATCTTCCACTTTG
*
143013 TTCAATCCCACTAAACATTCTGGTAAATCTTCCATTTTG
1 TTCAATCCCACTAAACATTCTGGTAAATCTTCCACTTTG
143052 TT
1 TT
143054 GACTGCCTGA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.23, C:0.25, G:0.10, T:0.42
Consensus pattern (39 bp):
TTCAATCCCACTAAACATTCTGGTAAATCTTCCACTTTG
Found at i:144624 original size:2 final size:2
Alignment explanation
Indices: 144619--144655 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
144609 TGTGATTATC
*
144619 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
144656 TATTTTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:145350 original size:19 final size:19
Alignment explanation
Indices: 145310--145352 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
145300 TTTTATAGTG
* *
145310 ATAAAATTATATAATATAT
1 ATAAAAATATAAAATATAT
145329 ATAAAAATATAAAAGTATTAT
1 ATAAAAATATAAAA-TA-TAT
145350 ATA
1 ATA
145353 TTTTATAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 12 0.60
20 2 0.10
21 6 0.30
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.37
Consensus pattern (19 bp):
ATAAAAATATAAAATATAT
Found at i:147474 original size:15 final size:15
Alignment explanation
Indices: 147454--147483 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
147444 GCGATCGTAA
*
147454 AGCTATAATTATTAT
1 AGCTATAATCATTAT
147469 AGCTATAATCATTAT
1 AGCTATAATCATTAT
147484 TTAACATAGA
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:0.40, C:0.10, G:0.07, T:0.43
Consensus pattern (15 bp):
AGCTATAATCATTAT
Found at i:147692 original size:20 final size:20
Alignment explanation
Indices: 147641--147683 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
147631 CATACCCACT
147641 ATTATTTTTTAAAATTTATA
1 ATTATTTTTTAAAATTTATA
*
147661 ATTATTTTTTAAATTTTA-A
1 ATTATTTTTTAAAATTTATA
147680 ATTA
1 ATTA
147684 ATTTATTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
ATTATTTTTTAAAATTTATA
Found at i:147723 original size:29 final size:28
Alignment explanation
Indices: 147673--147727 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 28
147663 TATTTTTTAA
*
147673 ATTTTAAATTAATTTATTAATGATATATC
1 ATTTTAAATTAATTTATCAATG-TATATC
*
147702 ATTTTAATATTTATTT-TCAATGTATA
1 ATTTTAA-ATTAATTTATCAATGTATA
147728 AATTTATACA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 4 0.17
29 12 0.52
30 7 0.30
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.55
Consensus pattern (28 bp):
ATTTTAAATTAATTTATCAATGTATATC
Found at i:148335 original size:16 final size:18
Alignment explanation
Indices: 148316--148348 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
148306 TTTATCATCG
148316 TATTTAA-A-AAATTTTA
1 TATTTAATATAAATTTTA
148332 TATTTAATATAAATTTT
1 TATTTAATATAAATTTT
148349 GATAAATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 1 0.07
18 7 0.47
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TATTTAATATAAATTTTA
Found at i:148558 original size:24 final size:23
Alignment explanation
Indices: 148517--148561 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
148507 GCAAGTGTAA
* *
148517 ATTTTAAAAATATTTTATTAATT
1 ATTTCAAAAATATGTTATTAATT
148540 ATTTCAAAAATTATGTTATTAA
1 ATTTCAAAAA-TATGTTATTAA
148562 AAATTATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
ATTTCAAAAATATGTTATTAATT
Found at i:149179 original size:26 final size:27
Alignment explanation
Indices: 149130--149192 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 27
149120 ATAAAAATTG
* *
149130 AAATTCTTTTATTAATTTGTTC-TTAC
1 AAATTTTTTTATTAATTTGCTCTTTAC
* *
149156 TATATTTTTTTCTTAATTT-CTCTTTAC
1 -AAATTTTTTTATTAATTTGCTCTTTAC
149183 AAATTTTTTT
1 AAATTTTTTT
149193 TACCTACCCT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
26 11 0.37
27 19 0.63
ACGTcount: A:0.24, C:0.11, G:0.02, T:0.63
Consensus pattern (27 bp):
AAATTTTTTTATTAATTTGCTCTTTAC
Found at i:150277 original size:10 final size:10
Alignment explanation
Indices: 150249--150280 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
150239 AATATTTTTA
150249 TTAATTAAAT
1 TTAATTAAAT
150259 TTAA-T-AAT
1 TTAATTAAAT
150267 TTAATTAAAT
1 TTAATTAAAT
150277 TTAA
1 TTAA
150281 AAAAAATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
8 7 0.35
9 2 0.10
10 11 0.55
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (10 bp):
TTAATTAAAT
Found at i:150684 original size:3 final size:3
Alignment explanation
Indices: 150676--150713 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
150666 AAAGTCAAGC
150676 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
150714 GTGGAGAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:151146 original size:23 final size:23
Alignment explanation
Indices: 151120--151190 Score: 79
Period size: 23 Copynumber: 2.9 Consensus size: 23
151110 ACGAAGAGAT
151120 ATAATATAAAAATAATTAAAAAA
1 ATAATATAAAAATAATTAAAAAA
*
151143 ATAATATAAAAATAATATATCATAAA
1 ATAATATAAAAATAAT-TA--AAAAA
* *
151169 ATCAATATATAAATATTTAAAA
1 AT-AATATAAAAATAATTAAAA
151191 TTTTATATAA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
23 16 0.40
24 4 0.10
26 8 0.20
27 12 0.30
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (23 bp):
ATAATATAAAAATAATTAAAAAA
Found at i:151159 original size:11 final size:11
Alignment explanation
Indices: 151120--151161 Score: 66
Period size: 11 Copynumber: 3.7 Consensus size: 11
151110 ACGAAGAGAT
151120 ATAATATAAAA
1 ATAATATAAAA
*
151131 ATAATTAAAAAA
1 ATAA-TATAAAA
151143 ATAATATAAAA
1 ATAATATAAAA
151154 ATAATATA
1 ATAATATA
151162 TCATAAAATC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
11 18 0.64
12 10 0.36
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (11 bp):
ATAATATAAAA
Found at i:151224 original size:19 final size:17
Alignment explanation
Indices: 151176--151233 Score: 66
Period size: 18 Copynumber: 3.4 Consensus size: 17
151166 AAAATCAATA
*
151176 TATAAATATTTAAAATTT
1 TATATATATTT-AAATTT
151194 TATATA-ATTTAAATTAT
1 TATATATATTTAAATT-T
151211 TAATATATATTTAAA-TT
1 T-ATATATATTTAAATTT
151228 TATATA
1 TATATA
151234 AAAATATAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
16 10 0.28
17 8 0.22
18 11 0.31
19 7 0.19
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TATATATATTTAAATTT
Found at i:151805 original size:19 final size:19
Alignment explanation
Indices: 151768--151852 Score: 61
Period size: 19 Copynumber: 4.5 Consensus size: 19
151758 TTTGAATTTT
*
151768 AATTTTTATATTATAATTA
1 AATTTTAATATTATAATTA
* *
151787 AATTTTAATATTTTTATT-
1 AATTTTAATATTATAATTA
* *
151805 AATTCATAA-ATT-TAATTT
1 AATT-TTAATATTATAATTA
*
151823 AATTTATAATATTATAA-AA
1 AATTT-TAATATTATAATTA
151842 ATATTTTAATA
1 A-ATTTTAATA
151853 ACTTAATTGA
Statistics
Matches: 52, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
17 4 0.08
18 14 0.27
19 27 0.52
20 7 0.13
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (19 bp):
AATTTTAATATTATAATTA
Found at i:151839 original size:26 final size:26
Alignment explanation
Indices: 151753--151840 Score: 72
Period size: 26 Copynumber: 3.2 Consensus size: 26
151743 TTGTACTCTA
*
151753 ATAAATTTGAATTTTAATTTTTATATT
1 ATAAATTT-AATTTTAATTTTAATATT
* *
151780 AT-AATTAAATTTTAATATTTTTATTAATT
1 ATAAATTTAATTTT-A-A-TTTTAAT-ATT
151809 CATAAATTTAA-TTTAATTTATAATATT
1 -ATAAATTTAATTTTAATTT-TAATATT
151836 ATAAA
1 ATAAA
151841 AATATTTTAA
Statistics
Matches: 49, Mismatches: 5, Indels: 15
0.71 0.07 0.22
Matches are distributed among these distances:
25 6 0.12
26 10 0.20
27 9 0.18
28 9 0.18
29 4 0.08
30 5 0.10
31 6 0.12
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (26 bp):
ATAAATTTAATTTTAATTTTAATATT
Found at i:153427 original size:21 final size:20
Alignment explanation
Indices: 153386--153433 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
153376 TATTAAATTA
153386 TAATTTAAATATAATAAAAT
1 TAATTTAAATATAATAAAAT
153406 TAATTTAAATTTATAA-AAAAT
1 TAATTTAAA--TATAATAAAAT
*
153427 TTATTTA
1 TAATTTA
153434 TAATCTAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 9 0.36
21 11 0.44
22 5 0.20
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TAATTTAAATATAATAAAAT
Found at i:154900 original size:32 final size:30
Alignment explanation
Indices: 154851--154909 Score: 73
Period size: 32 Copynumber: 1.9 Consensus size: 30
154841 ATTGCTTCTT
* *
154851 AAAAAATTATTATAAATAACTTTTTTATTTC
1 AAAAAATTATTAAAAATAA-TGTTTTATTTC
*
154882 AAAATAATTTTTAAAAATAATGTTTTAT
1 AAAA-AATTATTAAAAATAATGTTTTAT
154910 ATTTTTCTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 11 0.46
32 13 0.54
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.47
Consensus pattern (30 bp):
AAAAAATTATTAAAAATAATGTTTTATTTC
Found at i:155136 original size:2 final size:2
Alignment explanation
Indices: 155114--155162 Score: 73
Period size: 2 Copynumber: 25.0 Consensus size: 2
155104 AATAAGAACA
* *
155114 AT AT -T AT AC 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 AT AT AT AT AT
155155 AT AT AT AT
1 AT AT AT AT
155163 GAATTGGAGT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:156258 original size:21 final size:21
Alignment explanation
Indices: 156225--156265 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 21
156215 TTGATATATT
156225 AAATTAATTATATTTCTAAATAA
1 AAATTAA-TATATTTC-AAATAA
156248 AAATTAA-ATATTTCAAAT
1 AAATTAATATATTTCAAAT
156266 TACATCTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 7 0.39
23 7 0.39
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (21 bp):
AAATTAATATATTTCAAATAA
Found at i:157834 original size:14 final size:15
Alignment explanation
Indices: 157814--157854 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
157804 AAAACTAAAT
157814 ATATAATTTTTT-TA
1 ATATAATTTTTTATA
*
157828 TTATAATTATTTTATA
1 ATATAATT-TTTTATA
157844 ATATAATTTTT
1 ATATAATTTTT
157855 ATATGTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 7 0.30
15 7 0.30
16 9 0.39
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
ATATAATTTTTTATA
Found at i:157855 original size:14 final size:14
Alignment explanation
Indices: 157814--157857 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
157804 AAAACTAAAT
*
157814 ATATAATTTTTTTA
1 ATATAATTTTTATA
*
157828 TTATAATTATTTTATA
1 ATATAA-T-TTTTATA
157844 ATATAATTTTTATA
1 ATATAATTTTTATA
157858 TGTTTTAGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
14 12 0.48
15 2 0.08
16 11 0.44
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
ATATAATTTTTATA
Found at i:159040 original size:2 final size:2
Alignment explanation
Indices: 159033--159076 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
159023 TGTCATTTTG
*
159033 AT AT AT AT AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
159075 AT
1 AT
159077 GCATGCTTTG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:159243 original size:43 final size:44
Alignment explanation
Indices: 159195--159283 Score: 135
Period size: 44 Copynumber: 2.0 Consensus size: 44
159185 TCACAGCAAC
* *
159195 ATTGTGTAAATCGTGTG-GAATCTTGGTCATTTTCAAGGAAAAT
1 ATTGTGGAAATCGTGTGCAAATCTTGGTCATTTTCAAGGAAAAT
* *
159238 ATTGTGGAAATCTTGTGCAAATCTTGGTCCTTTTCAAGGAAAAT
1 ATTGTGGAAATCGTGTGCAAATCTTGGTCATTTTCAAGGAAAAT
159282 AT
1 AT
159284 CATGATTAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
43 15 0.37
44 26 0.63
ACGTcount: A:0.30, C:0.11, G:0.21, T:0.37
Consensus pattern (44 bp):
ATTGTGGAAATCGTGTGCAAATCTTGGTCATTTTCAAGGAAAAT
Found at i:159734 original size:43 final size:43
Alignment explanation
Indices: 159676--159764 Score: 115
Period size: 43 Copynumber: 2.1 Consensus size: 43
159666 TTAACCTTGA
* *
159676 AAAATATTATAGAAATCATGTTAAATCTTGATCTTTTTCAAAG
1 AAAATATTATAGAAATCATGTGAAATATTGATCTTTTTCAAAG
* * * * *
159719 AAAATATTGTGGAAATCGTGTGAAATATTGGTCTTTTTCAAGG
1 AAAATATTATAGAAATCATGTGAAATATTGATCTTTTTCAAAG
159762 AAA
1 AAA
159765 TTAAAAGTAG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.39, C:0.08, G:0.16, T:0.37
Consensus pattern (43 bp):
AAAATATTATAGAAATCATGTGAAATATTGATCTTTTTCAAAG
Found at i:160095 original size:4 final size:4
Alignment explanation
Indices: 160086--160113 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
160076 GAATTGTATT
160086 CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA
160114 TATATATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:160293 original size:32 final size:31
Alignment explanation
Indices: 160236--160349 Score: 140
Period size: 32 Copynumber: 3.6 Consensus size: 31
160226 ATATTGATAG
* *
160236 TAAATTTAAT-ATATTAGATATAATTACTTA
1 TAAATTTAATAATATTAAATATAATTATTTA
* *
160266 TATATTTAATAAATATTAAATAAAATTATTTA
1 TAAATTTAAT-AATATTAAATATAATTATTTA
160298 TAAATTTAATTAATATTAAATATAATTATTTA
1 TAAATTTAA-TAATATTAAATATAATTATTTA
* *
160330 AAAATTTAATTATCATTAAA
1 TAAATTTAATAAT-ATTAAA
160350 AAATTTTAAT
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
30 9 0.12
31 3 0.04
32 59 0.82
33 1 0.01
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (31 bp):
TAAATTTAATAATATTAAATATAATTATTTA
Found at i:160308 original size:16 final size:16
Alignment explanation
Indices: 160289--160342 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
160279 TATTAAATAA
160289 AATTATTTATAAATTT
1 AATTATTTATAAATTT
* *
160305 AATTA-ATATTAAATAT
1 AATTATTTA-TAAATTT
*
160321 AATTATTTAAAAATTT
1 AATTATTTATAAATTT
160337 AATTAT
1 AATTAT
160343 CATTAAAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
15 2 0.06
16 27 0.87
17 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
AATTATTTATAAATTT
Found at i:160485 original size:15 final size:15
Alignment explanation
Indices: 160467--160534 Score: 59
Period size: 14 Copynumber: 4.6 Consensus size: 15
160457 TATTTATTTC
*
160467 ATATTTAAAAATATT
1 ATATTTAAAAATAAT
* * *
160482 ATATAT-AAATTAAA
1 ATATTTAAAAATAAT
*
160496 ATATTTAAAATTAAAT
1 ATATTTAAAAAT-AAT
*
160512 AGATTT-AAAATAAT
1 ATATTTAAAAATAAT
160526 ATATTTAAA
1 ATATTTAAA
160535 TAAGAATAGT
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
14 18 0.44
15 16 0.39
16 7 0.17
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.41
Consensus pattern (15 bp):
ATATTTAAAAATAAT
Found at i:160504 original size:14 final size:14
Alignment explanation
Indices: 160482--160535 Score: 54
Period size: 15 Copynumber: 3.7 Consensus size: 14
160472 TAAAAATATT
*
160482 ATATATAAATTAAA
1 ATATTTAAATTAAA
160496 ATATTTAAAATTAAA
1 ATATTT-AAATTAAA
* * *
160511 TAGATTTAAAATAAT
1 -ATATTTAAATTAAA
160526 ATATTTAAAT
1 ATATTTAAAT
160536 AAGAATAGTA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
14 13 0.41
15 14 0.44
16 5 0.16
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (14 bp):
ATATTTAAATTAAA
Found at i:160543 original size:30 final size:30
Alignment explanation
Indices: 160487--160543 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
160477 ATATTATATA
* *
160487 TAAATTAAAATATTTAAAATTAAATAGATT
1 TAAAATAAAATATTTAAAATAAAATAGATT
*
160517 TAAAATAATATATTT-AAATAAGAATAG
1 TAAAATAAAATATTTAAAATAA-AATAG
160544 TACGACACTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 5 0.22
30 18 0.78
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (30 bp):
TAAAATAAAATATTTAAAATAAAATAGATT
Found at i:161752 original size:20 final size:20
Alignment explanation
Indices: 161705--161753 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
161695 TATTTATAAG
161705 TTAATTTTAAAAAAAATTTA
1 TTAATTTTAAAAAAAATTTA
**
161725 TATAATTTTAATGAAAA-TTA
1 T-TAATTTTAAAAAAAATTTA
161745 CTTAATTTT
1 -TTAATTTT
161754 CATACTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 11 0.44
21 14 0.56
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (20 bp):
TTAATTTTAAAAAAAATTTA
Found at i:162058 original size:10 final size:9
Alignment explanation
Indices: 162043--162128 Score: 61
Period size: 9 Copynumber: 9.2 Consensus size: 9
162033 ACAATTTATC
162043 TTATATATT
1 TTATATATT
162052 TTGATATA-T
1 TT-ATATATT
162061 TTATATA-T
1 TTATATATT
162069 TTATATTATTT
1 TTATA-TA-TT
162080 TTATATTATT
1 TTATA-TATT
162090 TT-TCATATT
1 TTAT-ATATT
*
162099 ATATCATATT
1 TTAT-ATATT
* *
162109 TGATATTTT
1 TTATATATT
*
162118 TTATTTATT
1 TTATATATT
162127 TT
1 TT
162129 TCATACCTTA
Statistics
Matches: 64, Mismatches: 7, Indels: 12
0.77 0.08 0.14
Matches are distributed among these distances:
8 11 0.17
9 25 0.39
10 19 0.30
11 9 0.14
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.66
Consensus pattern (9 bp):
TTATATATT
Found at i:162066 original size:8 final size:8
Alignment explanation
Indices: 162043--162086 Score: 52
Period size: 8 Copynumber: 5.1 Consensus size: 8
162033 ACAATTTATC
162043 TTATATATT
1 TTATATA-T
162052 TTGATATAT
1 TT-ATATAT
162061 TTATATAT
1 TTATATAT
162069 TTATATTAT
1 TTATA-TAT
*
162078 TTTTATAT
1 TTATATAT
162086 T
1 T
162087 ATTTTTCATA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
8 15 0.47
9 12 0.38
10 5 0.16
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (8 bp):
TTATATAT
Found at i:162097 original size:12 final size:11
Alignment explanation
Indices: 162068--162100 Score: 57
Period size: 11 Copynumber: 2.9 Consensus size: 11
162058 TATTTATATA
162068 TTTATATTATT
1 TTTATATTATT
162079 TTTATATTATT
1 TTTATATTATT
162090 TTTCATATTAT
1 TTT-ATATTAT
162101 ATCATATTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.67
12 7 0.33
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (11 bp):
TTTATATTATT
Found at i:162098 original size:37 final size:37
Alignment explanation
Indices: 162057--162133 Score: 106
Period size: 37 Copynumber: 2.1 Consensus size: 37
162047 ATATTTTGAT
162057 ATATT-TAT-ATATTT-ATATTATTTTTATATTATTTTTC
1 ATATTATATCATATTTGATA-T-TTTTTAT-TTATTTTTC
162094 ATATTATATCATATTTGATATTTTTTATTTATTTTTC
1 ATATTATATCATATTTGATATTTTTTATTTATTTTTC
162131 ATA
1 ATA
162134 CCTTATGTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
37 17 0.46
38 10 0.27
39 7 0.19
40 3 0.08
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.65
Consensus pattern (37 bp):
ATATTATATCATATTTGATATTTTTTATTTATTTTTC
Found at i:164161 original size:21 final size:21
Alignment explanation
Indices: 164122--164161 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
164112 AAAGATATAT
*
164122 TTAGATGAAAAGATGCATTGG
1 TTAGATGAAAAGATACATTGG
164143 TTAGATG-AAAGTATACATT
1 TTAGATGAAAAG-ATACATT
164162 TTTTAATGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.40, C:0.05, G:0.23, T:0.33
Consensus pattern (21 bp):
TTAGATGAAAAGATACATTGG
Found at i:165044 original size:54 final size:54
Alignment explanation
Indices: 164980--165086 Score: 205
Period size: 54 Copynumber: 2.0 Consensus size: 54
164970 ATAATTGATG
*
164980 CAAAGTTAAATTATTTAATATTTATGTGTAATAAATTAAAAAGATTGAATAAAA
1 CAAAGTTAAATTATTTAATATTTATGTGCAATAAATTAAAAAGATTGAATAAAA
165034 CAAAGTTAAATTATTTAATATTTATGTGCAATAAATTAAAAAGATTGAATAAA
1 CAAAGTTAAATTATTTAATATTTATGTGCAATAAATTAAAAAGATTGAATAAA
165087 TCTATGAATT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.51, C:0.03, G:0.09, T:0.36
Consensus pattern (54 bp):
CAAAGTTAAATTATTTAATATTTATGTGCAATAAATTAAAAAGATTGAATAAAA
Found at i:166251 original size:22 final size:23
Alignment explanation
Indices: 166212--166255 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
166202 TTTGAATTTT
*
166212 AAAAAATTAAATCGAAATTAAAC
1 AAAAAATTAAATCAAAATTAAAC
*
166235 AAAAAATTTAAT-AAAATTAAA
1 AAAAAATTAAATCAAAATTAAA
166256 TTTGATTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.68, C:0.05, G:0.02, T:0.25
Consensus pattern (23 bp):
AAAAAATTAAATCAAAATTAAAC
Found at i:166433 original size:43 final size:44
Alignment explanation
Indices: 166374--166471 Score: 107
Period size: 42 Copynumber: 2.3 Consensus size: 44
166364 ATTTAAATTA
* * * *
166374 ATTAAAATTTAAA--TA-AAAATAAAACTTAATTTAAATA-ATT
1 ATTAATATTTAAATTTATAAAATAAAAATTAAATTAAATATATC
* *
166414 A-TAATTTTTAAATTTATAAATTAAAAATTAAATTAAATATATC
1 ATTAATATTTAAATTTATAAAATAAAAATTAAATTAAATATATC
166457 ATTAATATTTAAATT
1 ATTAATATTTAAATT
166472 AAAATTAAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
39 9 0.20
40 1 0.02
41 2 0.04
42 19 0.41
43 3 0.07
44 12 0.26
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (44 bp):
ATTAATATTTAAATTTATAAAATAAAAATTAAATTAAATATATC
Found at i:166446 original size:5 final size:5
Alignment explanation
Indices: 166438--166513 Score: 53
Period size: 5 Copynumber: 13.8 Consensus size: 5
166428 TATAAATTAA
*
166438 AAATT AAATT AAATAT ATCATT AATATTT AAATT AAAATT AAATT AAATT
1 AAATT AAATT AAAT-T A-AATT AA-A-TT AAATT -AAATT AAATT AAATT
* * *
166488 TAATA AAATTT AAATCA AAATT AAAT
1 AAATT AAA-TT AAAT-T AAATT AAAT
166514 CGATACCTAC
Statistics
Matches: 56, Mismatches: 8, Indels: 14
0.72 0.10 0.18
Matches are distributed among these distances:
5 31 0.55
6 19 0.34
7 6 0.11
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (5 bp):
AAATT
Found at i:166479 original size:11 final size:11
Alignment explanation
Indices: 166430--166513 Score: 66
Period size: 11 Copynumber: 7.5 Consensus size: 11
166420 TTTAAATTTA
166430 TAAATTAAAAAT
1 TAAATT-AAAAT
166442 TAAATT-AAAT
1 TAAATTAAAAT
* *
166452 ATATCATTAATATT
1 -TA-AATTAA-AAT
166466 TAAATTAAAAT
1 TAAATTAAAAT
166477 TAAATT-AAAT
1 TAAATTAAAAT
*
166487 TTAA-TAAAATT
1 TAAATTAAAA-T
*
166498 TAAATCAAAAT
1 TAAATTAAAAT
166509 TAAAT
1 TAAAT
166514 CGATACCTAC
Statistics
Matches: 58, Mismatches: 7, Indels: 15
0.73 0.09 0.19
Matches are distributed among these distances:
9 1 0.02
10 14 0.24
11 20 0.34
12 18 0.31
13 3 0.05
14 2 0.03
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.39
Consensus pattern (11 bp):
TAAATTAAAAT
Found at i:166844 original size:29 final size:29
Alignment explanation
Indices: 166772--166847 Score: 88
Period size: 27 Copynumber: 2.7 Consensus size: 29
166762 TTATAAATTA
*
166772 ATATAAAAATATATTAAA-ATTTATATAAT
1 ATATAAAAATTTA-TAAATATTTATATAAT
*
166801 ATAT-AATATTT-TAAATA-TTATTATAAT
1 ATATAAAAATTTATAAATATTTA-TATAAT
166828 ATATAAAAATTTATAAATAT
1 ATATAAAAATTTATAAATAT
166848 AATATAAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
26 7 0.18
27 11 0.28
28 11 0.28
29 10 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (29 bp):
ATATAAAAATTTATAAATATTTATATAAT
Found at i:166857 original size:29 final size:29
Alignment explanation
Indices: 166772--166854 Score: 86
Period size: 28 Copynumber: 3.0 Consensus size: 29
166762 TTATAAATTA
* *
166772 ATATAAAAATATATTAAA-ATTTATATAAT
1 ATATAAAAATTTA-TAAATATATATATAAT
*
166801 ATAT-AATATTT-TAAATAT-TATTATAAT
1 ATATAAAAATTTATAAATATATA-TATAAT
166828 ATATAAAAATTTATAAATATA-ATATAA
1 ATATAAAAATTTATAAATATATATATAA
166855 ATAACATAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
26 6 0.13
27 12 0.26
28 16 0.35
29 12 0.26
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (29 bp):
ATATAAAAATTTATAAATATATATATAAT
Found at i:167145 original size:17 final size:19
Alignment explanation
Indices: 167123--167167 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
167113 AAATGCATCA
*
167123 TTAT-AATTAAA-ATTTAT
1 TTATAAATTAAATAATTAT
167140 TTATAAATTAAATAATTAT
1 TTATAAATTAAATAATTAT
167159 TTAATAAAT
1 TT-ATAAAT
167168 AATTTTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 4 0.17
18 7 0.29
19 7 0.29
20 6 0.25
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TTATAAATTAAATAATTAT
Found at i:168059 original size:18 final size:17
Alignment explanation
Indices: 168029--168067 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
168019 ATAAATATAA
*
168029 AAAT-AATTTAAATTATT
1 AAATAAATTAAAATT-TT
168046 AAATAAATTAAAATTTT
1 AAATAAATTAAAATTTT
168063 AAATA
1 AAATA
168068 TAAATAACAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AAATAAATTAAAATTTT
Found at i:168292 original size:4 final size:4
Alignment explanation
Indices: 168283--168322 Score: 64
Period size: 4 Copynumber: 10.2 Consensus size: 4
168273 GTATGCTTTT
*
168283 ATAA ATAA ATAA AT-C ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
168323 ATATACAGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
3 2 0.06
4 31 0.94
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAA
Found at i:169175 original size:15 final size:16
Alignment explanation
Indices: 169155--169190 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
169145 TCCAACCCAT
169155 ATATTATA-ATTAAAA
1 ATATTATATATTAAAA
169170 ATATTA-ATATTAAAA
1 ATATTATATATTAAAA
169185 A-ATTAT
1 ATATTAT
169191 TTTTATACTG
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATATTATATATTAAAA
Found at i:170206 original size:41 final size:39
Alignment explanation
Indices: 170098--170217 Score: 106
Period size: 41 Copynumber: 3.0 Consensus size: 39
170088 CTAAAGTCTC
*
170098 TTTTATTATTTAAAT-TAATAATAA--AAATAAAAATTAT
1 TTTTATTATTTAAATATAATAA-AATTAAATAAAAATAAT
*
170135 TTTTA-TA-TTAATATTTATAGTAAAATTTAAATAAAAATAAT
1 TTTTATTATTTAA-A--TATAATAAAA-TTAAATAAAAATAAT
* *
170176 TTTTATTATTTAAATAATAATCAAAATTAAATTAAATTAAT
1 TTTTATTATTTAAAT-ATAAT-AAAATTAAATAAAAATAAT
170217 T
1 T
170218 ATACTTAAAT
Statistics
Matches: 67, Mismatches: 5, Indels: 18
0.74 0.06 0.20
Matches are distributed among these distances:
35 4 0.06
36 3 0.04
37 5 0.07
38 3 0.04
39 5 0.07
40 1 0.01
41 35 0.52
42 7 0.10
43 4 0.06
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.47
Consensus pattern (39 bp):
TTTTATTATTTAAATATAATAAAATTAAATAAAAATAAT
Found at i:171282 original size:23 final size:22
Alignment explanation
Indices: 171256--171314 Score: 77
Period size: 20 Copynumber: 2.7 Consensus size: 22
171246 ATTTTAATTA
171256 TAAATATTAATATAAAACTATTT
1 TAAATATT-ATATAAAACTATTT
*
171279 TAAATATT-T-TAATACTATTT
1 TAAATATTATATAAAACTATTT
171299 TAAATAATTATATAAA
1 TAAAT-ATTATATAAA
171315 TTTTTGAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
20 15 0.48
21 4 0.13
22 1 0.03
23 11 0.35
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (22 bp):
TAAATATTATATAAAACTATTT
Found at i:171297 original size:11 final size:10
Alignment explanation
Indices: 171270--171302 Score: 50
Period size: 9 Copynumber: 3.3 Consensus size: 10
171260 TATTAATATA
171270 AAACTATTTT
1 AAACTATTTT
171280 AAA-TATTTT
1 AAACTATTTT
171289 AATACTATTTT
1 AA-ACTATTTT
171300 AAA
1 AAA
171303 TAATTATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
9 8 0.38
10 5 0.24
11 8 0.38
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (10 bp):
AAACTATTTT
Found at i:172408 original size:2 final size:2
Alignment explanation
Indices: 172395--172429 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
172385 ATTATCTTAG
*
172395 AT AT AC 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 A
172430 ACATATAGGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:173667 original size:32 final size:32
Alignment explanation
Indices: 173608--173711 Score: 115
Period size: 32 Copynumber: 3.3 Consensus size: 32
173598 TTAATAACTG
*
173608 TCAAATTTACGTGTAATTATATTTAATATTTA
1 TCAAATTTACGAGTAATTATATTTAATATTTA
* *
173640 TCAAATTTACGAGTAAATT-TATGTAATATTCA
1 TCAAATTTACGAGT-AATTATATTTAATATTTA
* * *
173672 TTAGATTTACAAGTAATTATATTTAAT-TTT-
1 TCAAATTTACGAGTAATTATATTTAATATTTA
*
173702 TTAAATTTAC
1 TCAAATTTAC
173712 AATCAATATC
Statistics
Matches: 61, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
30 9 0.15
31 6 0.10
32 42 0.69
33 4 0.07
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.48
Consensus pattern (32 bp):
TCAAATTTACGAGTAATTATATTTAATATTTA
Found at i:174083 original size:3 final size:3
Alignment explanation
Indices: 174075--174099 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
174065 AATGCATGCA
174075 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
174100 GTATACTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:175331 original size:22 final size:24
Alignment explanation
Indices: 175292--175342 Score: 72
Period size: 22 Copynumber: 2.2 Consensus size: 24
175282 TTAATTTAAA
*
175292 ATATT-TTTTTATATTATAAATAT
1 ATATTATTTTAATATTATAAATAT
175315 A-ATTATTTTAATA-TATAAATAT
1 ATATTATTTTAATATTATAAATAT
175337 ATATTA
1 ATATTA
175343 AAATATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
22 13 0.52
23 12 0.48
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
ATATTATTTTAATATTATAAATAT
Found at i:175341 original size:20 final size:21
Alignment explanation
Indices: 175281--175341 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 21
175271 TTAAGAAAGA
175281 TTTAAT-TTA-AAATAT-T-T
1 TTTAATATTATAAATATATAT
*
175298 TTTTATATTATAAATATAATTAT
1 TTTAATATTATAAATAT-A-TAT
175321 TTTAATA-TATAAATATATAT
1 TTTAATATTATAAATATATAT
175341 T
1 T
175342 AAAATATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
17 5 0.14
18 3 0.08
19 6 0.17
20 4 0.11
21 1 0.03
22 10 0.28
23 7 0.19
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TTTAATATTATAAATATATAT
Found at i:177465 original size:20 final size:20
Alignment explanation
Indices: 177437--177531 Score: 102
Period size: 20 Copynumber: 4.8 Consensus size: 20
177427 TTTTACCTTG
* *
177437 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTCTACA
* * *
177457 ATATATCGATACA-TGTATGA
1 ATGTATCGATACATTCTA-CA
*
177477 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTCTACA
*
177497 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTCTACA
*
177517 ATGTATCGTTACATT
1 ATGTATCGATACATT
177532 ATGTCTTTTT
Statistics
Matches: 63, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
19 2 0.03
20 58 0.92
21 3 0.05
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTCTACA
Found at i:178479 original size:22 final size:22
Alignment explanation
Indices: 178445--178498 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
178435 AGCCTTTGAC
178445 CATGCA-TTTTTTATTATGTTT
1 CATGCATTTTTTTATTATGTTT
178466 CATGCATTTTTTTATTATGTTT
1 CATGCATTTTTTTATTATGTTT
*
178488 TATGCATTTTT
1 CATGCATTTTT
178499 AACATGTCCA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 6 0.19
22 25 0.81
ACGTcount: A:0.19, C:0.09, G:0.09, T:0.63
Consensus pattern (22 bp):
CATGCATTTTTTTATTATGTTT
Found at i:182247 original size:78 final size:78
Alignment explanation
Indices: 182113--182320 Score: 222
Period size: 78 Copynumber: 2.7 Consensus size: 78
182103 GAGATAATAA
* * * * * * *
182113 CGGGGTTGGAGTGTTCCCTTGAAAATAACGGAGCTGGAGTATCCCTGGTTGTGAGAAATCGATGA
1 CGGGGTTGGAGTATTCCCTTGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAAT-A
*
182178 -TTAGAAAAAAAAT
65 TTTAGAAAAAAAAC
* * *
182191 CGGGATTGGAGTATCCCCTTGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATAT
1 CGGGGTTGGAGTATTCCCTTGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATA-
* * * *
182256 TTTGGGAATAAAGC
65 TTTAGAAAAAAAAC
* *
182270 CGGGGTTGGAGTATTCCC-TCAGAAGTAACGGGGTTGGAGTATCCCCGATTA
1 CGGGGTTGGAGTATTCCCTTGA-AAATAACGGGGTTGGAGTATCCCCGATTA
182321 AATAACAAGG
Statistics
Matches: 107, Mismatches: 20, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
77 1 0.01
78 55 0.51
79 51 0.48
ACGTcount: A:0.30, C:0.15, G:0.29, T:0.26
Consensus pattern (78 bp):
CGGGGTTGGAGTATTCCCTTGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATAT
TTAGAAAAAAAAC
Found at i:182326 original size:28 final size:27
Alignment explanation
Indices: 182270--182341 Score: 74
Period size: 28 Copynumber: 2.6 Consensus size: 27
182260 GGAATAAAGC
*
182270 CGGGGTTGGAGTATTCCCTCAGAAGTAA
1 CGGGGTTGGAGTA-TCCCTCAGAAATAA
*
182298 CGGGGTTGGAGTATCCC-CGATTAAATAA
1 CGGGGTTGGAGTATCCCTC-A-GAAATAA
**
182326 CAAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
182342 TCGACTATGA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
26 1 0.03
27 5 0.13
28 32 0.84
ACGTcount: A:0.26, C:0.18, G:0.31, T:0.25
Consensus pattern (27 bp):
CGGGGTTGGAGTATCCCTCAGAAATAA
Found at i:182391 original size:51 final size:50
Alignment explanation
Indices: 182329--182550 Score: 201
Period size: 51 Copynumber: 4.3 Consensus size: 50
182319 TAAATAACAA
* * * *
182329 GGTTGGAGTATCCTCGACTATGAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAATTGGT-GTTTTGGAAATAAAACCGG
* * * *
182380 AGTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTCGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT--ATGAAAATTGGTGTTTTGGAAATAAAACCGG
* * * *
182432 GGTTGGAGTATCCCTCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAACCGG
1 GGTTGGAGTATCCC-CGATTAT-G-AAAATTGGTGTTTTGGAAATAAAACCGG
* *** * ** *
182485 GGTTGGAATATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAGTCAG
1 GGTTGGAGTATCCCCGATTATG-AAAATTGGTGTTTTGGAAATAAAACCGG
182536 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
182551 TCGAAAATAA
Statistics
Matches: 139, Mismatches: 27, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
51 52 0.37
52 35 0.25
53 52 0.37
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (50 bp):
GGTTGGAGTATCCCCGATTATGAAAATTGGTGTTTTGGAAATAAAACCGG
Found at i:182461 original size:53 final size:49
Alignment explanation
Indices: 182329--182510 Score: 175
Period size: 53 Copynumber: 3.5 Consensus size: 49
182319 TAAATAACAA
* * * * *
182329 GGTTGGAGTATCCTCGACTATGAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAATTGG--TGTTTGAAAATAAAACCGG
* *
182380 AGTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTCGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT--ATGAAAATTGGTGTTT-GAAAATAAAACCGG
* * * *
182432 GGTTGGAGTATCCCTCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAACCGG
1 GGTTGGAGTATCCC-CGATTAT-G-AAAATTGGTGTTTGA-AAATAAAACCGG
*
182485 GGTTGGAATATCCCCGATTATGAAAA
1 GGTTGGAGTATCCCCGATTATGAAAA
182511 ATCAATATTT
Statistics
Matches: 109, Mismatches: 15, Indels: 15
0.78 0.11 0.11
Matches are distributed among these distances:
50 4 0.04
51 21 0.19
52 33 0.30
53 51 0.47
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (49 bp):
GGTTGGAGTATCCCCGATTATGAAAATTGGTGTTTGAAAATAAAACCGG
Found at i:182674 original size:133 final size:132
Alignment explanation
Indices: 182429--182683 Score: 311
Period size: 133 Copynumber: 1.9 Consensus size: 132
182419 AAAATAAAAC
* *
182429 CGGGGTTGGAGTATCCCTCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAACCGGGGTTGGAAT
1 CGGGGTTGGAGTATCCCTCGATTGTGGAAAAATTAGTGTTTTAGAAATAAAACCGGAGTTGGAAT
* * * *
182494 ATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAGTCAGGGTTGGAGTATCCCCTCGAAAAT
66 ATCCCCGATAATGAAAAATCAATATTTTGAAAATAAAATCAGGGTTGGAATATCCCCTCGAAAAT
182559 AA
131 AA
* * *
182561 CGGGGTTGGAGTATCCC-CGATTGT-GAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTGG
1 CGGGGTTGGAGTATCCCTCGATTGTGGAA-AAATTAGTG--TTTTAGAAATAAAACCGGAGTTGG
* * * * *
182624 AGTATCCCTGATAAT-AGAAAATTAGTGTTTTGAAAATAAAATC-GGAGTTGGAATATCCCC
63 AATATCCCCGATAATGA-AAAATCAATATTTTGAAAATAAAATCAGG-GTTGGAATATCCCC
182684 GATTGTGGAG
Statistics
Matches: 104, Mismatches: 14, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
130 3 0.03
131 15 0.14
132 20 0.19
133 66 0.63
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (132 bp):
CGGGGTTGGAGTATCCCTCGATTGTGGAAAAATTAGTGTTTTAGAAATAAAACCGGAGTTGGAAT
ATCCCCGATAATGAAAAATCAATATTTTGAAAATAAAATCAGGGTTGGAATATCCCCTCGAAAAT
AA
Found at i:185069 original size:13 final size:13
Alignment explanation
Indices: 185051--185076 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
185041 ACAAAGATCC
185051 ATGTATCGATACA
1 ATGTATCGATACA
185064 ATGTATCGATACA
1 ATGTATCGATACA
185077 CACAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:185140 original size:19 final size:18
Alignment explanation
Indices: 185116--185183 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
185106 CAGTAGCTAA
185116 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
185135 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
185150 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
185167 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
185184 TCGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:185156 original size:13 final size:13
Alignment explanation
Indices: 185138--185162 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
185128 ACAATACTTA
185138 TGTATCGATACAT
1 TGTATCGATACAT
185151 TGTATCGATACA
1 TGTATCGATACA
185163 AAACTTATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:185160 original size:32 final size:32
Alignment explanation
Indices: 185119--185181 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
185109 TAGCTAATTA
*
185119 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
185151 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
185182 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:185277 original size:20 final size:20
Alignment explanation
Indices: 185219--185319 Score: 143
Period size: 21 Copynumber: 5.0 Consensus size: 20
185209 GTTGGGACCC
185219 TGTATCGATACATTTGTAGAA
1 TGTATCGATACATTTGT-GAA
185240 TGTATCGATACA-TTGTGAA
1 TGTATCGATACATTTGTGAA
185259 TGTATCGATACATTTGTGAA
1 TGTATCGATACATTTGTGAA
***
185279 TGTATCGATACATTCTACAAA
1 TGTATCGATACATT-TGTGAA
185300 TGTATCGATACATTTG-GAA
1 TGTATCGATACATTTGTGAA
185319 T
1 T
185320 TTTTTTTTTC
Statistics
Matches: 73, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
19 18 0.25
20 26 0.36
21 29 0.40
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.38
Consensus pattern (20 bp):
TGTATCGATACATTTGTGAA
Found at i:185965 original size:55 final size:55
Alignment explanation
Indices: 185881--186668 Score: 1168
Period size: 55 Copynumber: 14.3 Consensus size: 55
185871 ATAAACTGTA
* * * * * *
185881 TCCTGCTCATTGAGGAGTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAA-AGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
185936 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
* *
185991 TCCTGCTCTTTGGGGAATGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
186046 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
* *
186101 TCCTGTTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
186156 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGGGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
*
186211 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
186266 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGGGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
* *
186321 TCCTACTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
186376 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
* *
186431 TCCTGCTCTTTAAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
186486 TCCTGCTCTTTGAGGACTGGAAGGCGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
186541 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
186596 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
186651 TCCTGCTCTTTGAGGACT
1 TCCTGCTCTTTGAGGACT
186669 AAAAAGCGGA
Statistics
Matches: 682, Mismatches: 36, Indels: 30
0.91 0.05 0.04
Matches are distributed among these distances:
54 21 0.03
55 641 0.94
56 20 0.03
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
Found at i:186045 original size:29 final size:28
Alignment explanation
Indices: 185955--186650 Score: 113
Period size: 28 Copynumber: 25.2 Consensus size: 28
185945 TTGAGGACTG
185955 AAAGGTGCCACCAACTTGTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
** * ** *
185983 GAAAGGTGTCCTGC-TCTT-TG-GGGAATG
1 -AAAGGTG-CCACCAACTTGTGTGGGCTTT
186010 AAAGGTGCCACCAACTTGTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
** * * * **
186038 AAGAGGTGTCCTGC-TCTT-TGAGGACTGG
1 AA-AGGTG-CCACCAACTTGTGTGGGCTTT
*
186066 AAA-ATGCCACCAACTTGTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
**** * * **
186093 GAAAGGTGTCC-TGTTCTT-TGAGGACTGG
1 -AAAGGTG-CCACCAACTTGTGTGGGCTTT
*
186121 AAA-ATGCCACCAACTTGTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
** * * * **
186148 AAGAGGTGTCCTGC-TCTT-TGAGGACTGG
1 AA-AGGTG-CCACCAACTTGTGTGGGCTTT
* *
186176 AAA-ATGCCACCAACTTGGGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
** * *
186203 GAAAGGTGTCCTGC-TCTT-TG-GGGAC-TG
1 -AAAGGTG-CCACCAACTTGTGTGGG-CTTT
186230 AAAGGTGCCACCAACTTGTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
** * * * **
186258 AAGAGGTGTCCTGC-TCTT-TGAGGACTGG
1 AA-AGGTG-CCACCAACTTGTGTGGGCTTT
* *
186286 AAA-ATGCCACCAACTTGGGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
* *
186313 GAAAGGTGTCCTA-C-TCTT-TG-GGGAC-TG
1 -AAAGGTG-CC-ACCAACTTGTGTGGG-CTTT
186340 AAAGGTGCCACCAACTTGTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
** * * * **
186368 AAGAGGTGTCCTGC-TCTT-TGAGGACTGG
1 AA-AGGTG-CCACCAACTTGTGTGGGCTTT
*
186396 AAA-ATGCCACCAACTTGTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
** * ** * **
186423 GAAAGGTGTCCTGC-TCTT-TAAGGACTGG
1 -AAAGGTG-CCACCAACTTGTGTGGGCTTT
*
186451 AAA-ATGCCACCAACTTGTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
** * * * *
186478 AAGAGGTGTCCTGC-TCTT-TGAGGAC-TG
1 AA-AGGTG-CCACCAACTTGTGTGGGCTTT
* *
186505 GAAGGCGCCACCAACTTGTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
** * *
186533 AAGAGGTGTCCTGC-TCTT-TG-GGGAC-TG
1 AA-AGGTG-CCACCAACTTGTGTGGG-CTTT
186560 AAAGGTGCCACCAACTTGTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
** * * * *
186588 AAGAGGTGTCCTGC-TCTT-TGAGGAC-TG
1 AA-AGGTG-CCACCAACTTGTGTGGGCTTT
186615 AAAGGTGCCACCAACTTGTGTGGGCTTT
1 AAAGGTGCCACCAACTTGTGTGGGCTTT
186643 AAGAGGTG
1 AA-AGGTG
186651 TCCTGCTCTT
Statistics
Matches: 435, Mismatches: 164, Indels: 136
0.59 0.22 0.19
Matches are distributed among these distances:
24 1 0.00
25 35 0.08
26 83 0.19
27 91 0.21
28 105 0.24
29 84 0.19
30 35 0.08
31 1 0.00
ACGTcount: A:0.21, C:0.20, G:0.31, T:0.29
Consensus pattern (28 bp):
AAAGGTGCCACCAACTTGTGTGGGCTTT
Found at i:186565 original size:26 final size:26
Alignment explanation
Indices: 186536--186621 Score: 68
Period size: 26 Copynumber: 3.2 Consensus size: 26
186526 GGGCTTTAAG
186536 AGGTGTCCTGCTCTTTGGGGACTGAA
1 AGGTGTCCTGCTCTTTGGGGACTGAA
** * *
186562 AGGTG-CCACCAACTTGTGTGGG-CTTTAA
1 AGGTGTCCTGC-TCTT-TG-GGGAC-TGAA
*
186590 GAGGTGTCCTGCTCTTTGAGGACTGAA
1 -AGGTGTCCTGCTCTTTGGGGACTGAA
186617 AGGTG
1 AGGTG
186622 CCACCAACTT
Statistics
Matches: 44, Mismatches: 9, Indels: 14
0.66 0.13 0.21
Matches are distributed among these distances:
25 3 0.07
26 13 0.30
27 8 0.18
28 9 0.20
29 8 0.18
30 3 0.07
ACGTcount: A:0.19, C:0.19, G:0.34, T:0.29
Consensus pattern (26 bp):
AGGTGTCCTGCTCTTTGGGGACTGAA
Found at i:187689 original size:35 final size:35
Alignment explanation
Indices: 187637--187704 Score: 95
Period size: 35 Copynumber: 1.9 Consensus size: 35
187627 TAAGTAGGTT
*
187637 TTTTCTTTTCTCTCTTTTTCTTTGTTTTGTTTTTTTG
1 TTTTCTTTTCTCTCTTTTT-TTTGCTTT-TTTTTTTG
187674 TTTT-TTTTC-CTCTTTTTTTTGCTTTTTTTTT
1 TTTTCTTTTCTCTCTTTTTTTTGCTTTTTTTTT
187705 GAAGAGAATG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 6 0.20
34 7 0.23
35 8 0.27
36 5 0.17
37 4 0.13
ACGTcount: A:0.00, C:0.13, G:0.06, T:0.81
Consensus pattern (35 bp):
TTTTCTTTTCTCTCTTTTTTTTGCTTTTTTTTTTG
Found at i:200168 original size:78 final size:79
Alignment explanation
Indices: 200063--200265 Score: 223
Period size: 78 Copynumber: 2.6 Consensus size: 79
200053 AATAACGGGG
* * * * * * *
200063 TTGGAGTGTTCCCTTGAAAATAACGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATGA-TTAG
1 TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAAT-ATTTAG
*
200127 AAAAAAAATC-AGGA
65 AAAAAAAAGCTAGGA
* * *
200141 TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGG
1 TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTAGA
* * * *
200206 GAATAAAGCTGGGG
66 AAAAAAAGCTAGGA
*
200220 TTGGAGTATCCCCTC-AGAAGTAACGGGGTTGGAGTATCCCCGATTA
1 TTGGAGTATCCCCTCGA-AAATAACGGGGTTGGAGTATCCCCGATTA
200266 AATAACAAGG
Statistics
Matches: 105, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
77 1 0.01
78 60 0.57
79 44 0.42
ACGTcount: A:0.31, C:0.16, G:0.28, T:0.26
Consensus pattern (79 bp):
TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTAGA
AAAAAAAGCTAGGA
Found at i:200370 original size:52 final size:53
Alignment explanation
Indices: 200309--200449 Score: 173
Period size: 52 Copynumber: 2.7 Consensus size: 53
200299 AATTGGTATT
* * *
200309 TTTG-GAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGG-AAAATTGGTG
1 TTTGAGAAATAAAACCGGGGTTGGAGTATCCCCGATTAAAGGAAAAATTAGTG
**
200360 TTTCGA-AAATAAAACCGGGGTTGGAGTATCCCCGATT-GTGGAAAAATTAGTG
1 TTT-GAGAAATAAAACCGGGGTTGGAGTATCCCCGATTAAAGGAAAAATTAGTG
* * *
200412 TTTTAGCAATAAAACCGGGGTTGGAATATCCCCGATTA
1 TTTGAGAAATAAAACCGGGGTTGGAGTATCCCCGATTA
200450 TGAAAAATCA
Statistics
Matches: 77, Mismatches: 8, Indels: 8
0.83 0.09 0.09
Matches are distributed among these distances:
51 6 0.08
52 71 0.92
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (53 bp):
TTTGAGAAATAAAACCGGGGTTGGAGTATCCCCGATTAAAGGAAAAATTAGTG
Found at i:200487 original size:51 final size:52
Alignment explanation
Indices: 200366--200475 Score: 150
Period size: 52 Copynumber: 2.1 Consensus size: 52
200356 GGTGTTTCGA
* * * * *
200366 AAATAAAACCGGGGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAG
1 AAATAAAACCGGGGTTGGAATATCCCCGATTATGGAAAAATCAATATTTTAG
* *
200418 CAATAAAACCGGGGTTGGAATATCCCCGATTAT-GAAAAATCAATATTTTGG
1 AAATAAAACCGGGGTTGGAATATCCCCGATTATGGAAAAATCAATATTTTAG
200469 AAATAAA
1 AAATAAA
200476 GTTGGGGTTG
Statistics
Matches: 50, Mismatches: 8, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
51 20 0.40
52 30 0.60
ACGTcount: A:0.38, C:0.13, G:0.22, T:0.27
Consensus pattern (52 bp):
AAATAAAACCGGGGTTGGAATATCCCCGATTATGGAAAAATCAATATTTTAG
Found at i:200577 original size:54 final size:51
Alignment explanation
Indices: 200510--200640 Score: 156
Period size: 51 Copynumber: 2.5 Consensus size: 51
200500 AAATAACGGG
* *
200510 GTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTG-AGAAATTAGTG--TTTTGAAAATAAAATCGGA
* *
200564 GTTGTAGTATCCCCGATTAT-AGAAAATTAGTGTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAG-AAATTAGTGTTTTGAAAATAAAATCGGA
* *
200615 GTTGGAATATCCCCAATTGTGGAGAA
1 GTTGGAGTATCCCCGATTGT-GAGAA
200641 TTGAGAAACT
Statistics
Matches: 66, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
51 34 0.52
52 4 0.06
53 10 0.15
54 18 0.27
ACGTcount: A:0.33, C:0.11, G:0.24, T:0.32
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTGTGAGAAATTAGTGTTTTGAAAATAAAATCGGA
Found at i:200619 original size:133 final size:131
Alignment explanation
Indices: 200375--200620 Score: 316
Period size: 133 Copynumber: 1.9 Consensus size: 131
200365 AAAATAAAAC
* *
200375 CGGGGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAACCGGGGTTGGAATA
1 CGGGGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGAAATAAAACCGGAGTTGGAATA
* * * *
200440 TCCCCGATTATGAAAAATCAATATTTTGGAAATAAAGTTGGGGTTGGAGTATTCCCTCGGAAATA
66 TCCCCGATTATGAAAAATCAATATTTTGAAAATAAAATCGGAGTTGGAGTATTCCCTCGGAAATA
200505 A
131 A
* * * *
200506 CGGGGTTGGAGTATCCCCGATTGT-GAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTGTA
1 CGGGGTTGGAGTATCCCCGATTGTGGAA-AAATTAGTG--TTTTAGAAATAAAACCGGAGTTGGA
* * * *
200570 GTATCCCCGATTAT-AGAAAATTAGTGTTTTGAAAATAAAATCGGAGTTGGA
63 ATATCCCCGATTATGA-AAAATCAATATTTTGAAAATAAAATCGGAGTTGGA
200621 ATATCCCCAA
Statistics
Matches: 97, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
130 3 0.03
131 32 0.33
132 1 0.01
133 61 0.63
ACGTcount: A:0.32, C:0.11, G:0.26, T:0.30
Consensus pattern (131 bp):
CGGGGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGAAATAAAACCGGAGTTGGAATA
TCCCCGATTATGAAAAATCAATATTTTGAAAATAAAATCGGAGTTGGAGTATTCCCTCGGAAATA
A
Found at i:203087 original size:19 final size:18
Alignment explanation
Indices: 203063--203130 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
203053 CAGTAGCTAA
203063 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
203082 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
203097 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
203114 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
203131 TCGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:203103 original size:13 final size:13
Alignment explanation
Indices: 203085--203109 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
203075 ACAATACTTA
203085 TGTATCGATACAT
1 TGTATCGATACAT
203098 TGTATCGATACA
1 TGTATCGATACA
203110 AAACTTATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:203107 original size:32 final size:32
Alignment explanation
Indices: 203066--203128 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
203056 TAGCTAATTA
*
203066 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
203098 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
203129 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:208224 original size:27 final size:27
Alignment explanation
Indices: 208185--208517 Score: 495
Period size: 27 Copynumber: 12.1 Consensus size: 27
208175 AGTGTGACCT
* *
208185 CTTTAAAGCCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
208212 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
* * *
208240 CTTTTAAGTCCACAACTTCATGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCACC
**
208267 CTTTTAAAGTCCACAACTCCGTGGCATT
1 CTTTT-AAGTCCACAACTCCGTGGCACC
208295 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
208322 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
208349 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
* * *
208377 CTTTTAAGACCACAACTCTGTAGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
208404 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* * *
208431 CTTTTAAGTCCATAACTCTGTGGCATCT
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
208459 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
208486 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
208514 CTTT
1 CTTT
208518 CAAAGCCCAC
Statistics
Matches: 279, Mismatches: 22, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
27 156 0.56
28 123 0.44
ACGTcount: A:0.23, C:0.34, G:0.14, T:0.29
Consensus pattern (27 bp):
CTTTTAAGTCCACAACTCCGTGGCACC
Found at i:208271 original size:55 final size:54
Alignment explanation
Indices: 208185--208517 Score: 495
Period size: 55 Copynumber: 6.1 Consensus size: 54
208175 AGTGTGACCT
* *
208185 CTTTAAAGCCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCA-CC
* * * **
208240 CTTTTAAGTCCACAACTTCATGGCATCCTTTTAAAGTCCACAACTCCGTGGCATT
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCACC
208295 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
* * *
208349 CTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGACCACAACTCTGTAGCACC
1 CTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCACC
* * *
208404 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCATAACTCTGTGGCATCT
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCA-CC
*
208459 CTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCACC
208514 CTTT
1 CTTT
208518 CAAAGCCCAC
Statistics
Matches: 251, Mismatches: 23, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
54 69 0.27
55 144 0.57
56 38 0.15
ACGTcount: A:0.23, C:0.34, G:0.14, T:0.29
Consensus pattern (54 bp):
CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
Found at i:208381 original size:82 final size:82
Alignment explanation
Indices: 208185--208517 Score: 508
Period size: 82 Copynumber: 4.0 Consensus size: 82
208175 AGTGTGACCT
* *
208185 CTTTAAAGCCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGT
1 CTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGT
* * *
208249 CCACAACTTCATGGCATC
65 CCACAACTCCGTGGCACC
*
208267 CTTTTAAAGTCCACAACTCCGTGGCAT-TCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGT
1 CTTTT-AAGTCCACAACTCCGTGGCATCCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGT
208331 CCACAACTCCGTGGCACC
65 CCACAACTCCGTGGCACC
* * *
208349 CTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGACCACAACTCTGTAGCACCCTTTTAAGTC
1 CTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
208414 CACAACTCCGTGGCACC
66 CACAACTCCGTGGCACC
* * * *
208431 CTTTTAAGTCCATAACTCTGTGGCATCTCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAAGT
1 CTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGT
208496 CCACAACTCCGTGGCACC
65 CCACAACTCCGTGGCACC
208514 CTTT
1 CTTT
208518 CAAAGCCCAC
Statistics
Matches: 232, Mismatches: 15, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
81 21 0.09
82 141 0.61
83 70 0.30
ACGTcount: A:0.23, C:0.34, G:0.14, T:0.29
Consensus pattern (82 bp):
CTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTC
CACAACTCCGTGGCACC
Found at i:208522 original size:28 final size:27
Alignment explanation
Indices: 208185--208784 Score: 439
Period size: 28 Copynumber: 21.5 Consensus size: 27
208175 AGTGTGACCT
*
208185 CTTTAAAGCCCACAACTCCGTGGCACC
1 CTTTAAAGCCCACAACTCAGTGGCACC
* * *
208212 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTAAAGCCCACAACTCAGTGGCA-CC
* *
208240 CTTTTAAGTCCACAACTTCA-TGGCATCC
1 CTTTAAAGCCCACAAC-TCAGTGGCA-CC
* * * **
208268 TTTTAAAGTCCACAACTCCGTGGCATT
1 CTTTAAAGCCCACAACTCAGTGGCACC
* * *
208295 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTAAAGCCCACAACTCAGTGGCACC
* * *
208322 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTAAAGCCCACAACTCAGTGGCACC
* * *
208349 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTAAAGCCCACAACTCAGTGGCA-CC
* * * *
208377 CTTTTAAGACCACAACTCTGTAGCACC
1 CTTTAAAGCCCACAACTCAGTGGCACC
* * *
208404 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTAAAGCCCACAACTCAGTGGCACC
* * * * *
208431 CTTTTAAGTCCATAACTCTGTGGCATCT
1 CTTTAAAGCCCACAACTCAGTGGCA-CC
* * *
208459 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTAAAGCCCACAACTCAGTGGCACC
* *
208486 CTTTTAAAGTCCACAACTCCGTGGCACC
1 C-TTTAAAGCCCACAACTCAGTGGCACC
*
208514 CTTTCAAAGCCCACACAAGTCAGTGGCACTC
1 CTTT-AAAG-CC-CACAACTCAGTGGCAC-C
* *
208545 CTTTCAAAGCCCACGCAAGTCAGTGGCACA
1 CTTT-AAAGCCCA--CAACTCAGTGGCACC
* * * * *
208575 TTTTCAAAGCCCACGAGTCAATGGCACT
1 CTTT-AAAGCCCACAACTCAGTGGCACC
*
208603 CTTTCAAAGCCCACAAGTCAGTGGCACC
1 CTTT-AAAGCCCACAACTCAGTGGCACC
* * * *
208631 CTTTCAAGCCCACGAGTCAGTGGTACC
1 CTTTAAAGCCCACAACTCAGTGGCACC
* * * *
208658 TTTTCAAAGCCCACGAGTTAGTGGCA-C
1 CTTT-AAAGCCCACAACTCAGTGGCACC
* *
208685 CTTTCAAAGCCCACAAGTCAGTGGCACT
1 CTTT-AAAGCCCACAACTCAGTGGCACC
* * *
208713 CTTTCAAAGCCCACGAGTCAGTGGCATC
1 CTTT-AAAGCCCACAACTCAGTGGCACC
* *
208741 CTTTCGAAGCCCACGCAAGTCAGTGGCACC
1 CTTT-AAAGCCCA--CAACTCAGTGGCACC
208771 CTTTTAAAGCCCAC
1 C-TTTAAAGCCCAC
208785 GCAAGTCAGT
Statistics
Matches: 501, Mismatches: 55, Indels: 33
0.85 0.09 0.06
Matches are distributed among these distances:
27 201 0.40
28 219 0.44
29 5 0.01
30 49 0.10
31 27 0.05
ACGTcount: A:0.25, C:0.34, G:0.16, T:0.25
Consensus pattern (27 bp):
CTTTAAAGCCCACAACTCAGTGGCACC
Found at i:208649 original size:55 final size:56
Alignment explanation
Indices: 208478--208794 Score: 361
Period size: 55 Copynumber: 5.5 Consensus size: 56
208468 CCACAACTCT
* * * * * *
208478 GTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTCAAAGCCCACACAAGTCA
1 GTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAG-CC-CACGAGTCA
**
208536 GTGGCACTCCTTTCAAAGCCCACGCAAGTCAGTGGCACATTTTCAAAGCCCACGAGTCA
1 GTGGCACT-CTTTCAAAGCCCA--CAAGTCAGTGGCACCCTTTCAAAGCCCACGAGTCA
*
208595 ATGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTC-AAGCCCACGAGTCA
1 GTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACGAGTCA
* * * *
208650 GTGGTAC-CTTTTCAAAGCCCACGAGTTAGTGGCA-CCTTTCAAAGCCCACAAGTCA
1 GTGGCACTC-TTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACGAGTCA
* * *
208705 GTGGCACTCTTTCAAAGCCCACGAGTCAGTGGCATCCTTTCGAAGCCCACGCAAGTCA
1 GTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACG--AGTCA
* *
208763 GTGGCACCCTTTTAAAGCCCACGCAAGTCAGT
1 GTGGCACTCTTTCAAAGCCCA--CAAGTCAGT
208795 AACACTATTT
Statistics
Matches: 225, Mismatches: 23, Indels: 20
0.84 0.09 0.07
Matches are distributed among these distances:
54 7 0.03
55 85 0.38
56 33 0.15
58 44 0.20
59 26 0.12
60 10 0.04
61 20 0.09
ACGTcount: A:0.26, C:0.33, G:0.20, T:0.21
Consensus pattern (56 bp):
GTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACGAGTCA
Found at i:208669 original size:83 final size:84
Alignment explanation
Indices: 208478--208835 Score: 400
Period size: 83 Copynumber: 4.1 Consensus size: 84
208468 CCACAACTCT
* * * *
208478 GTGGCACCCTTTT-AAAGTCCACAACTCCGTGGCACCCTTTCAAAGCCCACACAAGTCAGTGGCA
1 GTGGCA-CCTTTTCAAAGCCCACGAGTCAGTGGCACCCTTTCAAAG-CC-CACAAGTCAGTGGCA
208542 CTCCTTTCAAAGCCCACGCAAGTCA
63 C-CCTTTCAAAGCCCACG--AGTCA
* * *
208567 GTGGCACATTTTCAAAGCCCACGAGTCAATGGCACTCTTTCAAAGCCCACAAGTCAGTGGCACCC
1 GTGGCACCTTTTCAAAGCCCACGAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCC
208632 TTTC-AAGCCCACGAGTCA
66 TTTCAAAGCCCACGAGTCA
* * *
208650 GTGGTACCTTTTCAAAGCCCACGAGTTAGTGGCA-CCTTTCAAAGCCCACAAGTCAGTGGCACTC
1 GTGGCACCTTTTCAAAGCCCACGAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCC
208714 TTTCAAAGCCCACGAGTCA
66 TTTCAAAGCCCACGAGTCA
* * **
208733 GTGGCATCC-TTTCGAAGCCCACGCAAGTCAGTGGCACCCTTTTAAAGCCCACGCAAGTCAGTAA
1 GTGGCA-CCTTTTCAAAGCCCACG--AGTCAGTGGCACCCTTTCAAAGCCCA--CAAGTCAGTGG
** *
208797 CACTATTTTCAAAGCCCACATGTGTCA
61 CAC-CCTTTCAAAGCCCAC--GAGTCA
*
208824 GTGGCAACTTTT
1 GTGGCACCTTTT
208836 TTTCAAAGCC
Statistics
Matches: 234, Mismatches: 23, Indels: 22
0.84 0.08 0.08
Matches are distributed among these distances:
82 32 0.14
83 67 0.29
84 2 0.01
85 19 0.08
86 19 0.08
87 16 0.07
88 19 0.08
89 45 0.19
90 1 0.00
91 14 0.06
ACGTcount: A:0.27, C:0.32, G:0.19, T:0.22
Consensus pattern (84 bp):
GTGGCACCTTTTCAAAGCCCACGAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCC
TTTCAAAGCCCACGAGTCA
Found at i:210437 original size:22 final size:22
Alignment explanation
Indices: 210403--210456 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
210393 AGCCTTTGAC
210403 CATGCA-TTTTTTATTATGTTA
1 CATGCATTTTTTTATTATGTTA
*
210424 CATGCATTTTTTTATTATGTTT
1 CATGCATTTTTTTATTATGTTA
210446 CATGCATTTTT
1 CATGCATTTTT
210457 AACATGTCCA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 6 0.19
22 25 0.81
ACGTcount: A:0.20, C:0.11, G:0.09, T:0.59
Consensus pattern (22 bp):
CATGCATTTTTTTATTATGTTA
Found at i:214025 original size:6 final size:6
Alignment explanation
Indices: 213980--214027 Score: 53
Period size: 6 Copynumber: 8.2 Consensus size: 6
213970 TCTAATCAGA
* * * *
213980 TAAAA- TAAATT TAAATT TAAATT TAAACT TAAAAT TAAAAT TAAAAT
1 TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT
214027 T
1 T
214028 TTTTTCAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
5 4 0.10
6 35 0.90
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (6 bp):
TAAAAT
Found at i:215655 original size:25 final size:26
Alignment explanation
Indices: 215609--215657 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
215599 CACACCAACA
***
215609 AAACACAAACACCCACCCAAACAAAT
1 AAACACAAACACCCAAAAAAACAAAT
215635 AAACAC-AACACCCAAAAAAACAA
1 AAACACAAACACCCAAAAAAACAA
215658 CAAGCCCCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 14 0.70
26 6 0.30
ACGTcount: A:0.63, C:0.35, G:0.00, T:0.02
Consensus pattern (26 bp):
AAACACAAACACCCAAAAAAACAAAT
Found at i:215700 original size:8 final size:8
Alignment explanation
Indices: 215689--215738 Score: 52
Period size: 8 Copynumber: 6.5 Consensus size: 8
215679 CAACAACCAA
*
215689 AACAAGAC
1 AACAAAAC
215697 AACAAAAC
1 AACAAAAC
*
215705 AAAAAAAC
1 AACAAAAC
215713 -ACAAAA-
1 AACAAAAC
215719 AA-AAAAC
1 AACAAAAC
215726 AACAAACAC
1 AACAAA-AC
215735 AACA
1 AACA
215739 CACACCCAGA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
6 4 0.11
7 8 0.23
8 17 0.49
9 6 0.17
ACGTcount: A:0.76, C:0.22, G:0.02, T:0.00
Consensus pattern (8 bp):
AACAAAAC
Found at i:215713 original size:13 final size:13
Alignment explanation
Indices: 215686--215727 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
215676 ACACAACAAC
* *
215686 CAAAACAAGACAA
1 CAAAACAAAAAAA
215699 CAAAACAAAAAAA
1 CAAAACAAAAAAA
215712 CACAAA-AAAAAAA
1 CA-AAACAAAAAAA
215725 CAA
1 CAA
215728 CAAACACAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
12 1 0.04
13 22 0.85
14 3 0.12
ACGTcount: A:0.79, C:0.19, G:0.02, T:0.00
Consensus pattern (13 bp):
CAAAACAAAAAAA
Found at i:215724 original size:16 final size:18
Alignment explanation
Indices: 215675--215738 Score: 58
Period size: 18 Copynumber: 3.5 Consensus size: 18
215665 CAAGCCCCAC
* *
215675 AACACAAC-AACCAAAAC
1 AACACAACAAAACAAAAA
*
215692 AAGACAACAAAACAAAAA
1 AACACAACAAAACAAAAA
* *
215710 AACACAAAAAAAAAACAACA
1 AACACAACAAAACAA-AA-A
215730 AACACAACA
1 AACACAACA
215739 CACACCCAGA
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
17 7 0.19
18 19 0.51
19 2 0.05
20 9 0.24
ACGTcount: A:0.73, C:0.25, G:0.02, T:0.00
Consensus pattern (18 bp):
AACACAACAAAACAAAAA
Found at i:215787 original size:13 final size:14
Alignment explanation
Indices: 215767--215799 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
215757 AGCACACAAA
215767 CACCCACCCCCCCC
1 CACCCACCCCCCCC
215781 C-CCCACCCCCCCC
1 CACCCACCCCCCCC
215794 CACCCA
1 CACCCA
215800 ACACACCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 13 0.72
14 5 0.28
ACGTcount: A:0.15, C:0.85, G:0.00, T:0.00
Consensus pattern (14 bp):
CACCCACCCCCCCC
Found at i:215931 original size:23 final size:24
Alignment explanation
Indices: 215900--215963 Score: 78
Period size: 23 Copynumber: 2.8 Consensus size: 24
215890 ACACCCACAC
215900 CACCAACACCAACCACACAAAACA
1 CACCAACACCAACCACACAAAACA
* *
215924 -ACCAACACCAACAAC-CACAACA
1 CACCAACACCAACCACACAAAACA
* *
215946 CCCCAACCCCAACCACAC
1 CACCAACACCAACCACAC
215964 CCACCCAACA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
22 6 0.18
23 26 0.79
24 1 0.03
ACGTcount: A:0.48, C:0.52, G:0.00, T:0.00
Consensus pattern (24 bp):
CACCAACACCAACCACACAAAACA
Found at i:216152 original size:14 final size:15
Alignment explanation
Indices: 216135--216190 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 15
216125 CCAACAACAC
216135 AAAAAAC-AAACAAA
1 AAAAAACAAAACAAA
216149 AAAAAACAAAAC-AA
1 AAAAAACAAAACAAA
* *
216163 AAAACACAGAAC-AA
1 AAAAAACAAAACAAA
*
216177 AACAAACAAAACAA
1 AAAAAACAAAACAA
216191 CAACCCACCA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
14 30 0.86
15 5 0.14
ACGTcount: A:0.80, C:0.18, G:0.02, T:0.00
Consensus pattern (15 bp):
AAAAAACAAAACAAA
Found at i:216161 original size:19 final size:19
Alignment explanation
Indices: 216137--216187 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
216127 AACAACACAA
216137 AAAACAAACAAAAAAAAAC
1 AAAACAAACAAAAAAAAAC
* *
216156 AAAACAAA-AAACACAGAAC
1 AAAACAAACAAA-AAAAAAC
216175 AAAACAAACAAAA
1 AAAACAAACAAAA
216188 CAACAACCCA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 3 0.11
19 22 0.79
20 3 0.11
ACGTcount: A:0.80, C:0.18, G:0.02, T:0.00
Consensus pattern (19 bp):
AAAACAAACAAAAAAAAAC
Found at i:216178 original size:28 final size:27
Alignment explanation
Indices: 216130--216190 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 27
216120 CCCAACCAAC
216130 AACACAAAAAACAAACAAAAAAAAACAA
1 AACA-AAAAAACAAACAAAAAAAAACAA
*
216158 AACAAAAAACACAGAAC-AAAACAAACAA
1 AACAAAAAA-ACA-AACAAAAAAAAACAA
216186 AACAA
1 AACAA
216191 CAACCCACCA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
27 5 0.17
28 22 0.73
29 3 0.10
ACGTcount: A:0.79, C:0.20, G:0.02, T:0.00
Consensus pattern (27 bp):
AACAAAAAAACAAACAAAAAAAAACAA
Found at i:216180 original size:5 final size:5
Alignment explanation
Indices: 216127--216190 Score: 60
Period size: 5 Copynumber: 13.0 Consensus size: 5
216117 ACACCCAACC
* * * * *
216127 AACAA CACAA AAAACA AACAA AAAAA AACAA AACAA AA-AA CACAG AACAA
1 AACAA AACAA AACA-A AACAA AACAA AACAA AACAA AACAA AACAA AACAA
216177 AAC-A AACAA AACAA
1 AACAA AACAA AACAA
216191 CAACCCACCA
Statistics
Matches: 46, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
4 7 0.15
5 35 0.76
6 4 0.09
ACGTcount: A:0.78, C:0.20, G:0.02, T:0.00
Consensus pattern (5 bp):
AACAA
Done.