Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold72
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: 5928628
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 261288 characters in sequence are not A, C, G, or T
File 26 of 39
Found at i:3776152 original size:19 final size:19
Alignment explanation
Indices: 3776115--3776154 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
3776105 GTAATATGAA
*
3776115 TTTTTATATAATTTTATAT
1 TTTTTATATAATTTCATAT
3776134 TTTTTATAT-ATTATCATAT
1 TTTTTATATAATT-TCATAT
3776153 TT
1 TT
3776155 AAAATTATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 3 0.16
19 16 0.84
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTTTATATAATTTCATAT
Found at i:3776623 original size:21 final size:21
Alignment explanation
Indices: 3776597--3776645 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
3776587 TATTATATTT
3776597 TTATATTT-TATAATATTATAA
1 TTATATTTATATAAT-TTATAA
*
3776618 TTATATTTAATATAATTTATAT
1 TTATATTT-ATATAATTTATAA
3776640 TTATAT
1 TTATAT
3776646 AAATTTTAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 8 0.32
22 11 0.44
23 6 0.24
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TTATATTTATATAATTTATAA
Found at i:3776628 original size:18 final size:16
Alignment explanation
Indices: 3776616--3776650 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
3776606 ATAATATTAT
3776616 AATTATATTTAATATA
1 AATTATATTTAATATA
*
3776632 ATTTATATTT-ATATA
1 AATTATATTTAATATA
3776647 AATT
1 AATT
3776651 TTAATACATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
AATTATATTTAATATA
Found at i:3776631 original size:15 final size:15
Alignment explanation
Indices: 3776589--3776647 Score: 59
Period size: 15 Copynumber: 3.9 Consensus size: 15
3776579 TGTATTTATA
* *
3776589 TTATATTTTTATATT
1 TTATATTTATATAAT
*
3776604 TTATA-ATATTATAA-
1 TTATATTTA-TATAAT
3776618 TTATATTTAATATAAT
1 TTATATTT-ATATAAT
3776634 TTATATTTATATAA
1 TTATATTTATATAA
3776648 ATTTTAATAC
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 6 0.17
15 21 0.58
16 9 0.25
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TTATATTTATATAAT
Found at i:3776645 original size:6 final size:6
Alignment explanation
Indices: 3776581--3776645 Score: 53
Period size: 6 Copynumber: 10.5 Consensus size: 6
3776571 ATAATTTATG
* * *
3776581 TATTTA TATTATA TTTTTA TATTTTA TAATATTA TAATTA TATTTA -ATATA
1 TATTTA TATT-TA TATTTA TA-TTTA T-AT-TTA TATTTA TATTTA TATTTA
3776632 -ATTTA TATTTA TAT
1 TATTTA TATTTA TAT
3776646 AAATTTTAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
5 8 0.17
6 23 0.48
7 12 0.25
8 5 0.10
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (6 bp):
TATTTA
Found at i:3776681 original size:32 final size:32
Alignment explanation
Indices: 3776629--3776721 Score: 123
Period size: 32 Copynumber: 2.8 Consensus size: 32
3776619 TATATTTAAT
*
3776629 ATAATTTATATTTATATAAATTTTAATACATTG
1 ATAATTTATA-TTATATAAATTTTAATACATTA
* *
3776662 ATAATTTATATTATATAAATTTTAAAATATTA
1 ATAATTTATATTATATAAATTTTAATACATTA
*
3776694 ATATATTTATATCATATAAAATTTTAAT
1 ATA-ATTTATATTATAT-AAATTTTAAT
3776722 TATTTTTATG
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
32 22 0.42
33 22 0.42
34 9 0.17
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.51
Consensus pattern (32 bp):
ATAATTTATATTATATAAATTTTAATACATTA
Found at i:3776713 original size:26 final size:27
Alignment explanation
Indices: 3776684--3776737 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
3776674 ATATAAATTT
3776684 TAAAATATTAA-TATATTTATATCATA
1 TAAAATATTAATTATATTTATATCATA
* * *
3776710 TAAAATTTTAATTATTTTTATGTCATA
1 TAAAATATTAATTATATTTATATCATA
3776737 T
1 T
3776738 TTATATAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 10 0.42
27 14 0.58
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.52
Consensus pattern (27 bp):
TAAAATATTAATTATATTTATATCATA
Found at i:3778473 original size:15 final size:15
Alignment explanation
Indices: 3778453--3778481 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3778443 CATGAATTAT
3778453 GCTTTGCCATCTTAA
1 GCTTTGCCATCTTAA
3778468 GCTTTGCCATCTTA
1 GCTTTGCCATCTTA
3778482 CCAAACTTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.28, G:0.14, T:0.41
Consensus pattern (15 bp):
GCTTTGCCATCTTAA
Found at i:3779008 original size:19 final size:19
Alignment explanation
Indices: 3778986--3779040 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 19
3778976 ATATTATTTT
3778986 TATATTTATATATTAAATA
1 TATATTTATATATTAAATA
*
3779005 TATATTCATATCA-T-AATA
1 TATATTTATAT-ATTAAATA
*
3779023 TCATATTT-TATTTTAAAT
1 T-ATATTTATATATTAAAT
3779041 TATTTGATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 8
0.73 0.08 0.20
Matches are distributed among these distances:
18 9 0.31
19 19 0.66
20 1 0.03
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (19 bp):
TATATTTATATATTAAATA
Found at i:3779744 original size:211 final size:210
Alignment explanation
Indices: 3779383--3779878 Score: 750
Period size: 212 Copynumber: 2.4 Consensus size: 210
3779373 ATCTAGACTA
* * * * *
3779383 TGATTAAAGGAAAAACAATGGCAT-AAGGGGTGTTTGAAATTCCAAAAAAAAAAAATTAAGGGTC
1 TGATTAAAAGAAAAATAATGGCATGAAGGGGTGTATGAAATACC-AAAAAAAAAAATTAAGGGTA
3779447 ATTTTT-AAAAATATATACTTTTTAAAAAATATAAAAAATTAAAAGATAAAAATATTTTTGTTAT
65 ATTTTTAAAAAATATATACTTTTTAAAAAATATAAAAAATTAAAAGATAAAAATATTTTTGTTAT
*
3779511 ATAATTTAATATTAATATTTATTTTTTT-GTATAA-CTTTTGTAATTAGTTTAATATACTAAATA
130 ATAATTTAATATTAATATTTATTTTTTTCGTACAATC-TTTGTAATTAGTTTAATATACTAAATA
* *
3779574 TTTGTAGTTCCATACCG
194 TTTGTAGATCCAGACCG
*
3779591 TGATTAAAAGAAAAATAATGGCATGAAGGGGTGTATGAAATACCAAAAAAAAAATTTAAGGGTAA
1 TGATTAAAAGAAAAATAATGGCATGAAGGGGTGTATGAAATACCAAAAAAAAAAATTAAGGGTAA
*
3779656 TTTTTAAAAAATATATAATTTTTTCAAAAAATATAAAAAATTAAAAGATAAAAATATTTTTGTTA
66 TTTTTAAAAAATATAT-ACTTTTT-AAAAAATATAAAAAATTAAAAGATAAAAATATTTTTGTTA
* *
3779721 TATAATTTAATATTAATATTTATTTTTTTCGTACCATCTTTGTAATTTGTTTAATATACTAAATA
129 TATAATTTAATATTAATATTTATTTTTTTCGTACAATCTTTGTAATTAGTTTAATATACTAAATA
**
3779786 TTTGTAGATCCAGACTT
194 TTTGTAGATCCAGACCG
*** *
3779803 TGATTATGTGAAAAATAATGGCATGAAAGGGTGTATGAAATACCAAAAAAAAAAATTAAGGGTAA
1 TGATTAAAAGAAAAATAATGGCATGAAGGGGTGTATGAAATACCAAAAAAAAAAATTAAGGGTAA
*
3779868 -TTATAAAAAAT
66 TTTTTAAAAAAT
3779879 TAAAAGATAA
Statistics
Matches: 262, Mismatches: 20, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
208 46 0.18
209 27 0.10
210 6 0.02
211 79 0.30
212 103 0.39
213 1 0.00
ACGTcount: A:0.46, C:0.05, G:0.12, T:0.37
Consensus pattern (210 bp):
TGATTAAAAGAAAAATAATGGCATGAAGGGGTGTATGAAATACCAAAAAAAAAAATTAAGGGTAA
TTTTTAAAAAATATATACTTTTTAAAAAATATAAAAAATTAAAAGATAAAAATATTTTTGTTATA
TAATTTAATATTAATATTTATTTTTTTCGTACAATCTTTGTAATTAGTTTAATATACTAAATATT
TGTAGATCCAGACCG
Found at i:3780228 original size:208 final size:208
Alignment explanation
Indices: 3779869--3780949 Score: 1374
Period size: 208 Copynumber: 5.3 Consensus size: 208
3779859 TAAGGGTAAT
* * *
3779869 TATAAAAAATTAAAAGATAAAAATACTTTTGTTATATAATTTAATGTTAATATTTA-TTTTTTGT
1 TATAAAAAATTAAAAGATAAAAATATTTTTGTTATATAATTTAATATTAATATTAATTTTTTTGT
* * * * *
3779933 ACTACTTTTGTAATTTGTTTAATATACTAAATATTTGTAAATCCAGATTGTGATTAAAGAAAAAA
66 ACCACTTTTGTAATTTGTTTAATATACTAAATATTTGTAGATCCAGACTATGATTAAAG-GAAAA
3779998 ATAATGGCATG-AAAGCGTGTATGAAATACCAAAAAAAAATTTAAGGGTAATTTTTTAAAAATAT
130 ATAATGGCATGAAAAG-GTGTATGAAATACCAAAAAAAAATTTAAGGGTAATTTTTTAAAAATAT
3780062 ATTTTTTTCAAAAAA
194 ATTTTTTTCAAAAAA
3780077 TATAAAAAATTAAAAGATAAAAATATTTTTGTTATATAATTTAATATTAATATTAATTTTTTTGT
1 TATAAAAAATTAAAAGATAAAAATATTTTTGTTATATAATTTAATATTAATATTAATTTTTTTGT
3780142 ACCACTTTTGTAATTTGTTTAATATACTAAATATTTGTAGATCCAGACTATGATTAAAGGAAAAA
66 ACCACTTTTGTAATTTGTTTAATATACTAAATATTTGTAGATCCAGACTATGATTAAAGGAAAAA
* * *
3780207 TATTGGCATGAAAGGGTGTATGAAATACCAAAAAAAAAGTTAAGGGTAA-TTTTTAAAAA-ATA-
131 TAATGGCATGAAAAGGTGTATGAAATACCAAAAAAAAATTTAAGGGTAATTTTTTAAAAATATAT
3780269 -----T--AAAAA
196 TTTTTTCAAAAAA
* * *
3780275 -AT-----A-TAAAA-ATAAAAATATTTTTGTTATATGATTTAATATTAATATTTACTTTTTTCG
1 TATAAAAAATTAAAAGATAAAAATATTTTTGTTATATAATTTAATATTAATA-TTAATTTTTTTG
* * * * * *
3780332 TATCACCTTTGTAATTTGTTTAATATACTAAATATTTATAAATGCAAACTATGATTAAAGGAAAA
65 TACCACTTTTGTAATTTGTTTAATATACTAAATATTTGTAGATCCAGACTATGATTAAAGG-AAA
* * * * * *
3780397 ATATAATGGCAAGAAAAGGTATATGAAATACC-AAAAAAAATTAAAAGGTTATTTTTAAAAAATA
129 A-ATAATGGCATGAAAAGGTGTATGAAATACCAAAAAAAAATTTAAGGGTAATTTTTTAAAAATA
3780461 TATAATTTTTTCAAAAAA
193 TAT--TTTTTTCAAAAAA
3780479 TATAAAAAATTAAAAGATAAAAATATTTTTGTTATATAATTTAATATTAATATGT-ATTTTTTTC
1 TATAAAAAATTAAAAGATAAAAATATTTTTGTTATATAATTTAATATTAATAT-TAATTTTTTT-
* * * *
3780543 ATACCACTTTTGTAATTTGTTTAATATACTAAATATTTGTAGA-CCTAGACTGTGACTAAAGGGA
64 GTACCACTTTTGTAATTTGTTTAATATACTAAATATTTGTAGATCC-AGACTATGATTAAAGGAA
* * ** *
3780607 AAATAATAGCATGAAAAGGTGTTTGAAATA-TTAAAAAAAA-TTAAAGGTAA-TTTTTAAAAATT
128 AAATAATGGCATGAAAAGGTGTATGAAATACCAAAAAAAAATTTAAGGGTAATTTTTTAAAAA-T
3780669 ATATAATTTTTTCAAAAAA
192 ATAT--TTTTTTCAAAAAA
* * *
3780688 TATAAAAAATTTAAAGATAAAAATATTTTTGTTATATAATTTAATATTAATATTTA-TTTTTTAT
1 TATAAAAAATTAAAAGATAAAAATATTTTTGTTATATAATTTAATATTAATATTAATTTTTTTGT
* * * * *
3780752 A--ACCTTTGTAATTTATTTAATATACTAAATATTTGTAGATCCAAACTATAATTAAAAGAAAAA
66 ACCACTTTTGTAATTTGTTTAATATACTAAATATTTGTAGATCCAGACTATGATTAAAGGAAAAA
* * * * * *
3780815 TAATAGCATGAAAAGGTATTTGAAATACTAAAAAAAAATTAAAGGGTAATTTTTAAAAAGTATAT
131 TAATGGCATGAAAAGGTGTATGAAATACCAAAAAAAAATTTAAGGGTAATTTTTTAAAA--ATAT
3780880 AATTTTTTTCAAAAAA
194 -ATTTTTTTCAAAAAA
3780896 TATAAAAAATTAAAAGATAAAAATATTTTTGTTATATAATTTAATATTAATATT
1 TATAAAAAATTAAAAGATAAAAATATTTTTGTTATATAATTTAATATTAATATT
3780950 TTTATATTTT
Statistics
Matches: 770, Mismatches: 65, Indels: 76
0.85 0.07 0.08
Matches are distributed among these distances:
190 35 0.05
191 70 0.09
192 20 0.03
193 35 0.05
194 3 0.00
197 2 0.00
198 5 0.01
200 1 0.00
202 1 0.00
204 5 0.01
205 79 0.10
206 14 0.02
207 21 0.03
208 190 0.25
209 150 0.19
210 36 0.05
211 16 0.02
212 87 0.11
ACGTcount: A:0.47, C:0.05, G:0.09, T:0.39
Consensus pattern (208 bp):
TATAAAAAATTAAAAGATAAAAATATTTTTGTTATATAATTTAATATTAATATTAATTTTTTTGT
ACCACTTTTGTAATTTGTTTAATATACTAAATATTTGTAGATCCAGACTATGATTAAAGGAAAAA
TAATGGCATGAAAAGGTGTATGAAATACCAAAAAAAAATTTAAGGGTAATTTTTTAAAAATATAT
TTTTTTCAAAAAA
Found at i:3780435 original size:191 final size:191
Alignment explanation
Indices: 3779675--3780873 Score: 1101
Period size: 209 Copynumber: 6.1 Consensus size: 191
3779665 AATATATAAT
*
3779675 TTTTTCAAAAAATATAAAAAAT-TAAAAGATAAAAATATTTTTGTTATATAATTTAATATTAATA
1 TTTTTAAAAAAATATAAAAAATATAAAAGATAAAAATATTTTTGTTATATAATTTAATATTAATA
* * *
3779739 TTTATTTTTTTCGTACCATCTTTGTAATTTGTTTAATATACTAAATATTTGTAGATCCAGACTTT
66 TTTA-TTTTTTCGTACCACCTTTGTAATTTGTTTAATATACTAAATATTTGTAGATCCAAACTAT
* * * * *
3779804 GATT-ATGTGAAAAATAATGGCATGAAAGGGTGTATGAAATACC-AAAAAAA--AAAA-TTAA
130 GATTAAAG-GAAAAATAATAGCATGAAAAGGTATATGAAATACCAAAAAAAATTAAAAGGTAA
*** * * *
3779862 -GGGT----AATTATAAAAAAT-TAAAAGATAAAAATACTTTTGTTATATAATTTAATGTTAATA
1 TTTTTAAAAAAATATAAAAAATATAAAAGATAAAAATATTTTTGTTATATAATTTAATATTAATA
* * * * * *
3779921 TTTATTTTTT-GTACTACTTTTGTAATTTGTTTAATATACTAAATATTTGTAAATCCAGATTGTG
66 TTTATTTTTTCGTACCACCTTTGTAATTTGTTTAATATACTAAATATTTGTAGATCCAAACTATG
* * * * *
3779985 ATTAAAGAAAAAAATAATGGCATG-AAAGCGTGTATGAAATACCAAAAAAAAATTTAAGGGTAA
131 ATTAAAG-GAAAAATAATAGCATGAAAAG-GTATATGAAATACC-AAAAAAAATTAAAAGGTAA
*
3780048 TTTTTTAAAAATATATTTTTTTCAAAAAATATAAAAAATTAAAAGATAAAAATATTTTTGTTATA
1 -TTTTTAAAAA-A-A----TAT--AAAAA-AT-----A-TAAAAGATAAAAATATTTTTGTTATA
* * *
3780113 TAATTTAATATTAATATTAATTTTTTTGTACCACTTTTGTAATTTGTTTAATATACTAAATATTT
50 TAATTTAATATTAATATTTATTTTTTCGTACCACCTTTGTAATTTGTTTAATATACTAAATATTT
* * * * *
3780178 GTAGATCCAGACTATGATTAAAGGAAAAATATTGGCATGAAAGGGTGTATGAAATACCAAAAAAA
115 GTAGATCCAAACTATGATTAAAGGAAAAATAATAGCATGAAAAGGTATATGAAATACC-AAAAAA
*
3780243 AAGTT-AAGGGTAA
179 AA-TTAAAAGGTAA
*
3780256 TTTTT-AAAAAATATAAAAAATATAAAA-ATAAAAATATTTTTGTTATATGATTTAATATTAATA
1 TTTTTAAAAAAATATAAAAAATATAAAAGATAAAAATATTTTTGTTATATAATTTAATATTAATA
* * * *
3780319 TTTACTTTTTTCGTATCACCTTTGTAATTTGTTTAATATACTAAATATTTATAAATGCAAACTAT
66 TTTA-TTTTTTCGTACCACCTTTGTAATTTGTTTAATATACTAAATATTTGTAGATCCAAACTAT
* * *
3780384 GATTAAAGGAAAAATATAATGGCAAGAAAAGGTATATGAAATACCAAAAAAAATTAAAAGGTTA
130 GATTAAAGG-AAAA-ATAATAGCATGAAAAGGTATATGAAATACCAAAAAAAATTAAAAGGTAA
3780448 TTTTTAAAAAATATATAATTTTTTCAAAAAATATAAAAAATTAAAAGATAAAAATATTTTTGTTA
1 TTTTT-AAAAA-A-AT-A-----T--AAAAA-AT-----A-TAAAAGATAAAAATATTTTTGTTA
* * *
3780513 TATAATTTAATATTAATATGTATTTTTTTCATACCACTTTTGTAATTTGTTTAATATACTAAATA
48 TATAATTTAATATTAATATTTA-TTTTTTCGTACCACCTTTGTAATTTGTTTAATATACTAAATA
* * * * * * **
3780578 TTTGTAGA-CCTAGACTGTGACTAAAGGGAAAATAATAGCATGAAAAGGTGTTTGAAATATTAAA
112 TTTGTAGATCC-AAACTATGATTAAAGGAAAAATAATAGCATGAAAAGGTATATGAAATACCAAA
3780642 AAAAATT-AAAGGTAA
176 AAAAATTAAAAGGTAA
3780657 TTTTTAAAAATTATATAATTTTTTCAAAAAATATAAAAAATTTAAAGATAAAAATATTTTTGTTA
1 TTTTTAAAAA--A-AT-A-----T-AAAAAATAT-----A---AAAGATAAAAATATTTTTGTTA
* *
3780722 TATAATTTAATATTAATATTTATTTTTT-ATA--ACCTTTGTAATTTATTTAATATACTAAATAT
48 TATAATTTAATATTAATATTTATTTTTTCGTACCACCTTTGTAATTTGTTTAATATACTAAATAT
* * * *
3780784 TTGTAGATCCAAACTATAATTAAAAGAAAAATAATAGCATGAAAAGGTATTTGAAATACTAAAAA
113 TTGTAGATCCAAACTATGATTAAAGGAAAAATAATAGCATGAAAAGGTATATGAAATAC-CAAAA
*
3780849 AAAATTAAAGGGTAA
177 AAAATTAAAAGGTAA
3780864 TTTTTAAAAA
1 TTTTTAAAAA
3780874 GTATATAATT
Statistics
Matches: 859, Mismatches: 84, Indels: 118
0.81 0.08 0.11
Matches are distributed among these distances:
180 54 0.06
181 37 0.04
182 56 0.07
183 7 0.01
185 2 0.00
186 4 0.00
188 1 0.00
190 38 0.04
191 69 0.08
192 25 0.03
193 27 0.03
194 4 0.00
195 1 0.00
196 2 0.00
197 3 0.00
198 7 0.01
200 7 0.01
201 3 0.00
202 2 0.00
204 6 0.01
205 80 0.09
206 17 0.02
207 27 0.03
208 110 0.13
209 130 0.15
210 35 0.04
211 9 0.01
212 96 0.11
ACGTcount: A:0.46, C:0.05, G:0.10, T:0.39
Consensus pattern (191 bp):
TTTTTAAAAAAATATAAAAAATATAAAAGATAAAAATATTTTTGTTATATAATTTAATATTAATA
TTTATTTTTTCGTACCACCTTTGTAATTTGTTTAATATACTAAATATTTGTAGATCCAAACTATG
ATTAAAGGAAAAATAATAGCATGAAAAGGTATATGAAATACCAAAAAAAATTAAAAGGTAA
Found at i:3780723 original size:209 final size:207
Alignment explanation
Indices: 3780256--3780950 Score: 1022
Period size: 212 Copynumber: 3.3 Consensus size: 207
3780246 TTAAGGGTAA
*
3780256 TTTTT-AAAAAATATAAAAAATATAAAA-ATAAAAATATTTTTGTTATATGATTTAATATTAATA
1 TTTTTCAAAAAATATAAAAAAT-TAAAAGATAAAAATATTTTTGTTATATAATTTAATATTAATA
* * * *
3780319 TTTACTTTTTTCGTATCACCTTTGTAATTTGTTTAATATACTAAATATTTATAAATGCAAACTAT
65 TTTA-TTTTTTCATA-CACCTTTGTAATTTGTTTAATATACTAAATATTTGTAGATCCAAACTAT
* * * ** *
3780384 GATTAAAGGAAAAATATAATGGCAAGAAAAGGTATATGAAATACCAAAAAAAATTAAAAGGTTAT
128 GATTAAAGG-AAAA-ATAATAGCATGAAAAGGTATTTGAAATATAAAAAAAAATT-AAAGGTAAT
3780449 TTTTAAAAAATATATAAT
190 TTTTAAAAAATATATAAT
3780467 TTTTTCAAAAAATATAAAAAATTAAAAGATAAAAATATTTTTGTTATATAATTTAATATTAATAT
1 TTTTTCAAAAAATATAAAAAATTAAAAGATAAAAATATTTTTGTTATATAATTTAATATTAATAT
* * * *
3780532 GTATTTTTTTCATACCACTTTTGTAATTTGTTTAATATACTAAATATTTGTAGA-CCTAGACTGT
66 TTA-TTTTTTCATA-CACCTTTGTAATTTGTTTAATATACTAAATATTTGTAGATCC-AAACTAT
* * * *
3780596 GACTAAAGGGAAAATAATAGCATGAAAAGGTGTTTGAAATATTAAAAAAAATTAAAGGTAATTTT
128 GATTAAAGGAAAAATAATAGCATGAAAAGGTATTTGAAATATAAAAAAAAATTAAAGGTAATTTT
*
3780661 TAAAAATTATATAAT
193 TAAAAAATATATAAT
*
3780676 TTTTTCAAAAAATATAAAAAATTTAAAGATAAAAATATTTTTGTTATATAATTTAATATTAATAT
1 TTTTTCAAAAAATATAAAAAATTAAAAGATAAAAATATTTTTGTTATATAATTTAATATTAATAT
* *
3780741 TTATTTTTT-ATA-ACCTTTGTAATTTATTTAATATACTAAATATTTGTAGATCCAAACTATAAT
66 TTATTTTTTCATACACCTTTGTAATTTGTTTAATATACTAAATATTTGTAGATCCAAACTATGAT
*
3780804 TAAAAGAAAAATAATAGCATGAAAAGGTATTTGAAATACTAAAAAAAAATTAAAGGGTAATTTTT
131 TAAAGGAAAAATAATAGCATGAAAAGGTATTTGAAATA-TAAAAAAAAATTAAA-GGTAATTTTT
*
3780869 AAAAAGTATATAATT
194 AAAAAATATATAA-T
3780884 TTTTTCAAAAAATATAAAAAATTAAAAGATAAAAATATTTTTGTTATATAATTTAATATTAATAT
1 TTTTTCAAAAAATATAAAAAATTAAAAGATAAAAATATTTTTGTTATATAATTTAATATTAATAT
3780949 TT
66 TT
3780951 TTATATTTTT
Statistics
Matches: 442, Mismatches: 35, Indels: 17
0.89 0.07 0.03
Matches are distributed among these distances:
205 77 0.17
206 16 0.04
207 25 0.06
208 73 0.17
209 91 0.21
210 34 0.08
211 14 0.03
212 112 0.25
ACGTcount: A:0.48, C:0.05, G:0.08, T:0.40
Consensus pattern (207 bp):
TTTTTCAAAAAATATAAAAAATTAAAAGATAAAAATATTTTTGTTATATAATTTAATATTAATAT
TTATTTTTTCATACACCTTTGTAATTTGTTTAATATACTAAATATTTGTAGATCCAAACTATGAT
TAAAGGAAAAATAATAGCATGAAAAGGTATTTGAAATATAAAAAAAAATTAAAGGTAATTTTTAA
AAAATATATAAT
Found at i:3780996 original size:19 final size:19
Alignment explanation
Indices: 3780953--3780996 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
3780943 TAATATTTTT
*
3780953 ATATT-TTTAATTAAATTG
1 ATATTATTTAATTAAATAG
*
3780971 ATATTATTTAATTCAATAG
1 ATATTATTTAATTAAATAG
*
3780990 ATTTTAT
1 ATATTAT
3780997 AATCGTATGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 5 0.23
19 17 0.77
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.55
Consensus pattern (19 bp):
ATATTATTTAATTAAATAG
Found at i:3781494 original size:16 final size:15
Alignment explanation
Indices: 3781459--3781497 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
3781449 TAAAAAATAC
*
3781459 TTAAATATTATTTTA
1 TTAAATATTAATTTA
*
3781474 TTAAATTTTAATTTA
1 TTAAATATTAATTTA
3781489 TATAAATAT
1 T-TAAATAT
3781498 ATACATTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TTAAATATTAATTTA
Found at i:3782007 original size:42 final size:42
Alignment explanation
Indices: 3781926--3782015 Score: 128
Period size: 42 Copynumber: 2.1 Consensus size: 42
3781916 ACACTTGTAA
**
3781926 ATTTTTCACTTAAATGTTTGAAAAAAAAAAGGGTAAAATTTTT
1 ATTTTTCACTTAAATGAATG-AAAAAAAAAGGGTAAAATTTTT
*
3781969 ATTTTTCCACTTAAATGAATG-AAAAAAAATGGTAAAATTTTT
1 ATTTTT-CACTTAAATGAATGAAAAAAAAAGGGTAAAATTTTT
3782011 ATTTT
1 ATTTT
3782016 AAGTTCTTGA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
42 25 0.58
43 6 0.14
44 12 0.28
ACGTcount: A:0.43, C:0.06, G:0.10, T:0.41
Consensus pattern (42 bp):
ATTTTTCACTTAAATGAATGAAAAAAAAAGGGTAAAATTTTT
Found at i:3783305 original size:22 final size:22
Alignment explanation
Indices: 3783278--3783335 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 22
3783268 ATTAAAATTT
*
3783278 ATATAAATATATAATATTTTAA
1 ATATAAATATATAATATATTAA
**
3783300 ATAT-AAT-TACGATATATTAA
1 ATATAAATATATAATATATTAA
3783320 ATACATAAATATATAA
1 AT--ATAAATATATAA
3783336 ATTATTATAT
Statistics
Matches: 27, Mismatches: 5, Indels: 6
0.71 0.13 0.16
Matches are distributed among these distances:
20 12 0.44
21 3 0.11
22 6 0.22
23 3 0.11
24 3 0.11
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (22 bp):
ATATAAATATATAATATATTAA
Found at i:3783617 original size:13 final size:13
Alignment explanation
Indices: 3783599--3783628 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3783589 ATTTTTTTTG
*
3783599 TTATTAATATTTA
1 TTATTAATATATA
3783612 TTATTAATATATA
1 TTATTAATATATA
3783625 TTAT
1 TTAT
3783629 AATTAAACTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TTATTAATATATA
Found at i:3787085 original size:19 final size:19
Alignment explanation
Indices: 3787063--3787118 Score: 53
Period size: 18 Copynumber: 2.9 Consensus size: 19
3787053 TTGTTTATCT
3787063 AATTAAATAAATTATTTTA
1 AATTAAATAAATTATTTTA
*
3787082 AATT-AAT-AATTAAATTTA
1 AATTAAATAAATT-ATTTTA
* *
3787100 AATAAAAATATATTATTTT
1 AAT-TAAATAAATTATTTT
3787119 TGAATAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
17 4 0.14
18 11 0.38
19 4 0.14
20 7 0.24
21 3 0.10
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
AATTAAATAAATTATTTTA
Found at i:3791201 original size:42 final size:42
Alignment explanation
Indices: 3791142--3791224 Score: 166
Period size: 42 Copynumber: 2.0 Consensus size: 42
3791132 ACAACTCATC
3791142 AAGTTCTATTAATTCTGGAGAGAGAGCTGCTGAATTACAGCA
1 AAGTTCTATTAATTCTGGAGAGAGAGCTGCTGAATTACAGCA
3791184 AAGTTCTATTAATTCTGGAGAGAGAGCTGCTGAATTACAGC
1 AAGTTCTATTAATTCTGGAGAGAGAGCTGCTGAATTACAGC
3791225 TGGAACCAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.29
Consensus pattern (42 bp):
AAGTTCTATTAATTCTGGAGAGAGAGCTGCTGAATTACAGCA
Found at i:3796081 original size:21 final size:22
Alignment explanation
Indices: 3796057--3796100 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 22
3796047 TCTGCAAGAT
3796057 AAAGAAAGTTCAAA-A-AAGTTA
1 AAAGAAAG-TCAAATAGAAGTTA
3796078 AAAGAAAGTCAAATAGAAGTTA
1 AAAGAAAGTCAAATAGAAGTTA
3796100 A
1 A
3796101 TACAAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.61, C:0.05, G:0.16, T:0.18
Consensus pattern (22 bp):
AAAGAAAGTCAAATAGAAGTTA
Found at i:3799373 original size:2 final size:2
Alignment explanation
Indices: 3799366--3799410 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
3799356 GCCAGTAGGT
3799366 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
3799408 TA T
1 TA T
3799411 GTGTGTATAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3800485 original size:23 final size:22
Alignment explanation
Indices: 3800453--3800495 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
3800443 TTTTTATATT
*
3800453 TTTAAGATATAATATTTAATAAA
1 TTTAAAATATAAT-TTTAATAAA
3800476 TTTAAAATATAATTTTAATA
1 TTTAAAATATAATTTTAATA
3800496 TTTATAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (22 bp):
TTTAAAATATAATTTTAATAAA
Found at i:3801312 original size:3 final size:3
Alignment explanation
Indices: 3801304--3801366 Score: 94
Period size: 3 Copynumber: 21.0 Consensus size: 3
3801294 CATTGATTAC
3801304 AGA AGA AGA AGA AGA AGA AGA AG- AGCA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AG-A AGA AGA AGA AGA AGA AGA
3801349 AGA AGA AG- AGCA AGA AGA
1 AGA AGA AGA AG-A AGA AGA
3801367 TAGAGTGCGA
Statistics
Matches: 56, Mismatches: 0, Indels: 8
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.07
3 48 0.86
4 4 0.07
ACGTcount: A:0.63, C:0.03, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:3801680 original size:12 final size:12
Alignment explanation
Indices: 3801663--3801687 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3801653 TTTTTTTTTA
3801663 AAAGAGAGAGAG
1 AAAGAGAGAGAG
3801675 AAAGAGAGAGAG
1 AAAGAGAGAGAG
3801687 A
1 A
3801688 GAGAAGCTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (12 bp):
AAAGAGAGAGAG
Found at i:3803663 original size:20 final size:20
Alignment explanation
Indices: 3803638--3803675 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3803628 AAAGTATTTT
*
3803638 TATATAAATTTATTATAACA
1 TATATAAATTTAATATAACA
*
3803658 TATATAATTTTAATATAA
1 TATATAAATTTAATATAA
3803676 AAATGAGTAT
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:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (20 bp):
TATATAAATTTAATATAACA
Found at i:3804825 original size:36 final size:35
Alignment explanation
Indices: 3804780--3804857 Score: 90
Period size: 37 Copynumber: 2.2 Consensus size: 35
3804770 TTATGAATTT
*
3804780 AAAT-TTA-TTTTATTTAAATT-ATTATTTAATAATAA
1 AAATATTATTTTTATTTAAATTAATTA-TAAAT-AT-A
*
3804815 AAATATTATTTTTATTTAATTTAATTATAAATATA
1 AAATATTATTTTTATTTAAATTAATTATAAATATA
3804850 AAATATTA
1 AAATATTA
3804858 ATATAATTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
35 13 0.34
36 5 0.13
37 16 0.42
38 4 0.11
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (35 bp):
AAATATTATTTTTATTTAAATTAATTATAAATATA
Found at i:3804868 original size:19 final size:19
Alignment explanation
Indices: 3804835--3804878 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
3804825 TTTATTTAAT
3804835 TTAATTATAAATATAAAATA
1 TTAA-TATAAATATAAAATA
* *
3804855 TTAATATAATTATATAATA
1 TTAATATAAATATAAAATA
*
3804874 ATAAT
1 TTAAT
3804879 TTGATATCTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
TTAATATAAATATAAAATA
Found at i:3805025 original size:11 final size:11
Alignment explanation
Indices: 3805009--3805038 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
3804999 AAATTTAATA
3805009 ATTTATATTAT
1 ATTTATATTAT
3805020 ATTTATATTAT
1 ATTTATATTAT
*
3805031 TTTTATAT
1 ATTTATAT
3805039 CATAATCATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
ATTTATATTAT
Found at i:3805444 original size:11 final size:11
Alignment explanation
Indices: 3805428--3805466 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
3805418 ACTTGCCTAT
3805428 TATTATATTTA
1 TATTATATTTA
3805439 TATTATTTATTTA
1 TATTA--TATTTA
*
3805452 TATTATAATTA
1 TATTATATTTA
3805463 TATT
1 TATT
3805467 TAAAATGTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
11 14 0.56
13 11 0.44
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
TATTATATTTA
Found at i:3805451 original size:13 final size:14
Alignment explanation
Indices: 3805425--3805457 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
3805415 TAGACTTGCC
3805425 TATTATTATATTTA
1 TATTATTATATTTA
3805439 TATTATT-TATTTA
1 TATTATTATATTTA
3805452 TATTAT
1 TATTAT
3805458 AATTATATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TATTATTATATTTA
Found at i:3805519 original size:18 final size:17
Alignment explanation
Indices: 3805498--3805533 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
3805488 AAATTTTGCT
3805498 ATTTTATATATTAATATC
1 ATTTTATAT-TTAATATC
*
3805516 ATTTTATATTTTATATC
1 ATTTTATATTTAATATC
3805533 A
1 A
3805534 AAATTTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (17 bp):
ATTTTATATTTAATATC
Found at i:3805531 original size:25 final size:27
Alignment explanation
Indices: 3805474--3805531 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
3805464 ATTTAAAATG
* *
3805474 TTATTTATTAATATAAATTTTGCTATT
1 TTATATATTAATATAAATTTTGATATT
*
3805501 TTATATATTAATAT-CATTTT-ATATT
1 TTATATATTAATATAAATTTTGATATT
3805526 TTATAT
1 TTATAT
3805532 CAAAATTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 10 0.36
26 5 0.18
27 13 0.46
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.60
Consensus pattern (27 bp):
TTATATATTAATATAAATTTTGATATT
Found at i:3810038 original size:31 final size:31
Alignment explanation
Indices: 3810003--3810063 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
3809993 GGATAATAAA
* *
3810003 AAAATGGAGCAGAACTTTCAATAACTATAGC
1 AAAATGGAACACAACTTTCAATAACTATAGC
*
3810034 AAAATGGAATACAACTTTCAATAACTATAG
1 AAAATGGAACACAACTTTCAATAACTATAG
3810064 GAAGCTGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.48, C:0.15, G:0.13, T:0.25
Consensus pattern (31 bp):
AAAATGGAACACAACTTTCAATAACTATAGC
Found at i:3826044 original size:13 final size:14
Alignment explanation
Indices: 3826013--3826050 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
3826003 AATTAAAACT
3826013 AATTATATATAAGA
1 AATTATATATAAGA
*
3826027 AATTATAT-TAATA
1 AATTATATATAAGA
*
3826040 AATTAAATATA
1 AATTATATATA
3826051 TTTTTTATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (14 bp):
AATTATATATAAGA
Found at i:3826487 original size:19 final size:19
Alignment explanation
Indices: 3826441--3826480 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
3826431 TATTCATATC
* *
3826441 AAACACATATTTATATTCA
1 AAACATATATTTAAATTCA
*
3826460 AAACTTATATTTAAATTCA
1 AAACATATATTTAAATTCA
3826479 AA
1 AA
3826481 TAATATAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (19 bp):
AAACATATATTTAAATTCA
Found at i:3833135 original size:2 final size:2
Alignment explanation
Indices: 3833128--3833156 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3833118 AAAATGATTT
3833128 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3833157 CATCATTTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3846732 original size:3 final size:3
Alignment explanation
Indices: 3846688--3846716 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
3846678 GAAAATTTGT
3846688 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3846717 TTTACAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3847860 original size:2 final size:2
Alignment explanation
Indices: 3847853--3847899 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
3847843 AGATCTTCCA
* *
3847853 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3847895 AT AT A
1 AT AT A
3847900 AGCTTATAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3848966 original size:15 final size:16
Alignment explanation
Indices: 3848948--3848980 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
3848938 ATTTCTGTCA
3848948 TTTTATTAAT-AATTT
1 TTTTATTAATAAATTT
*
3848963 TTTTATTATTAAATTT
1 TTTTATTAATAAATTT
3848979 TT
1 TT
3848981 GAAATAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTTATTAATAAATTT
Found at i:3849193 original size:20 final size:20
Alignment explanation
Indices: 3849148--3849194 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
3849138 TTTATTTAAA
*
3849148 TAAAAATTGATACATTTATT
1 TAAAAATTAATACATTTATT
* *
3849168 TCAAAATTAATATA-TTATAT
1 TAAAAATTAATACATTTAT-T
3849188 TAAAAAT
1 TAAAAAT
3849195 AAATTTAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (20 bp):
TAAAAATTAATACATTTATT
Found at i:3853538 original size:2 final size:2
Alignment explanation
Indices: 3853531--3853568 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
3853521 CGCCTTTGTT
* *
3853531 TC TC TC TC TC TC TC TC TC TC TC TC TC TC GC TC GC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3853569 GATTTTCTCT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.05, T:0.45
Consensus pattern (2 bp):
TC
Found at i:3859312 original size:22 final size:23
Alignment explanation
Indices: 3859282--3859324 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
3859272 ATTTTTAAAT
*
3859282 TTATTTATTTTTAT-ATTAATAG
1 TTATATATTTTTATAATTAATAG
3859304 TTATATATTTTTATAATTAAT
1 TTATATATTTTTATAATTAAT
3859325 TTTTTATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (23 bp):
TTATATATTTTTATAATTAATAG
Found at i:3859705 original size:16 final size:17
Alignment explanation
Indices: 3859681--3859715 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
3859671 AGATTAGTTT
3859681 AATTAATTTAAT-TTAA
1 AATTAATTTAATATTAA
*
3859697 AATTTATTTAATATTAA
1 AATTAATTTAATATTAA
3859714 AA
1 AA
3859716 AAATTTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
AATTAATTTAATATTAA
Found at i:3859741 original size:28 final size:30
Alignment explanation
Indices: 3859690--3859754 Score: 84
Period size: 28 Copynumber: 2.3 Consensus size: 30
3859680 TAATTAATTT
*
3859690 AATTT-AAAATTTATTTAATATT-AAAA-A
1 AATTTAAAAATGTATTTAATATTAAAAATA
3859717 AATTTAAAAATGTATATTAAT-TTAAAAATA
1 AATTTAAAAATGTAT-TTAATATTAAAAATA
3859747 AATTTAAA
1 AATTTAAA
3859755 TAAAAATTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
27 5 0.15
28 10 0.30
29 9 0.27
30 9 0.27
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (30 bp):
AATTTAAAAATGTATTTAATATTAAAAATA
Found at i:3859755 original size:28 final size:27
Alignment explanation
Indices: 3859690--3859754 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 27
3859680 TAATTAATTT
*
3859690 AATTTAAAATTTATTTAATATTAAAAA
1 AATTTAAAATGTATTTAATATTAAAAA
3859717 AATTTAAAAATGTATATTAAT-TTAAAAATA
1 AATTT-AAAATGTAT-TTAATATT-AAAA-A
3859747 AATTTAAA
1 AATTTAAA
3859755 TAAAAATTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
27 5 0.15
28 10 0.30
29 12 0.36
30 6 0.18
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (27 bp):
AATTTAAAATGTATTTAATATTAAAAA
Found at i:3859774 original size:23 final size:22
Alignment explanation
Indices: 3859748--3859801 Score: 56
Period size: 23 Copynumber: 2.5 Consensus size: 22
3859738 TTAAAAATAA
*
3859748 ATTTAAATAAAAATTTAAAATTT
1 ATTTAAATAAAAAGTT-AAATTT
* *
3859771 ATTTAGATAATAAGTTAAATTT
1 ATTTAAATAAAAAGTTAAATTT
*
3859793 -TTTATATAA
1 ATTTAAATAA
3859802 TATTATTTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 8 0.30
22 6 0.22
23 13 0.48
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (22 bp):
ATTTAAATAAAAAGTTAAATTT
Found at i:3859940 original size:3 final size:3
Alignment explanation
Indices: 3859932--3859967 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
3859922 TTAGGTTTGG
3859932 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3859968 CAAAGGGCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:3867880 original size:3 final size:3
Alignment explanation
Indices: 3867872--3867924 Score: 97
Period size: 3 Copynumber: 17.7 Consensus size: 3
3867862 TTGCTGTATA
*
3867872 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAC
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3867920 AAT AA
1 AAT AA
3867925 CAGGCAAATA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:3870098 original size:29 final size:31
Alignment explanation
Indices: 3870024--3870099 Score: 86
Period size: 29 Copynumber: 2.5 Consensus size: 31
3870014 ATTTAGGTAG
*
3870024 AATTTTAAATAAATATTTTGTTTATTAAATTT
1 AATTTTAAA-AAATATTTTGTATATTAAATTT
**
3870056 AA-TTTAATTTAATATTTT-TAT-TTAAATTT
1 AATTTTAA-AAAATATTTTGTATATTAAATTT
3870085 AATTTTAAAAAATAT
1 AATTTTAAAAAATAT
3870100 AAATATTAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
29 15 0.41
30 7 0.19
31 13 0.35
32 2 0.05
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (31 bp):
AATTTTAAAAAATATTTTGTATATTAAATTT
Found at i:3871450 original size:23 final size:25
Alignment explanation
Indices: 3871395--3871450 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 25
3871385 AAAATAATTT
* *
3871395 AATTTATTGATAATATGTAAAATTA
1 AATTTATTAATAATATGTAAAAATA
*
3871420 TATATTATTAAT-ATAT-TAAAAATA
1 AAT-TTATTAATAATATGTAAAAATA
3871444 AATTTAT
1 AATTTAT
3871451 AAAAAATCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
23 4 0.15
24 9 0.35
25 6 0.23
26 7 0.27
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (25 bp):
AATTTATTAATAATATGTAAAAATA
Found at i:3874151 original size:2 final size:2
Alignment explanation
Indices: 3874144--3874218 Score: 94
Period size: 2 Copynumber: 41.5 Consensus size: 2
3874134 TGAACTTTAG
3874144 TA TA TA TA -A TA T- TA T- TA TA T- TA TA T- TA TA T- 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
3874180 T- TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3874219 GTGATTATCC
Statistics
Matches: 65, Mismatches: 0, Indels: 16
0.80 0.00 0.20
Matches are distributed among these distances:
1 8 0.12
2 57 0.88
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:3874290 original size:21 final size:20
Alignment explanation
Indices: 3874257--3874304 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 20
3874247 TAAAGTTATA
*
3874257 AAAAAATATATAG-AATATTT
1 AAAAAATAAATAGTAAT-TTT
3874277 AAAAAATAAAATAGTAATTTT
1 AAAAAAT-AAATAGTAATTTT
3874298 ATAAAAA
1 A-AAAAA
3874305 CGAATGGGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 7 0.29
21 9 0.38
22 8 0.33
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (20 bp):
AAAAAATAAATAGTAATTTT
Found at i:3874302 original size:23 final size:22
Alignment explanation
Indices: 3874252--3874304 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 22
3874242 TATATTAAAG
*
3874252 TTATAAAAAAATATATAGAATA
1 TTATAAAAAAATAAATAGAATA
*
3874274 TT-T-AAAAAATAAAATAGTAATT
1 TTATAAAAAAAT-AAATAG-AATA
3874296 TTATAAAAA
1 TTATAAAAA
3874305 CGAATGGGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
20 7 0.28
21 6 0.24
22 7 0.28
23 1 0.04
24 4 0.16
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (22 bp):
TTATAAAAAAATAAATAGAATA
Found at i:3875575 original size:15 final size:15
Alignment explanation
Indices: 3875555--3875596 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
3875545 ATTATTAAAT
3875555 TATTAATATTTTTTA
1 TATTAATATTTTTTA
*
3875570 TATTAATATATCTTTA
1 TATTAATAT-TTTTTA
3875586 TAATTAA-ATTT
1 T-ATTAATATTT
3875597 AAATAAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 10 0.43
16 8 0.35
17 5 0.22
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (15 bp):
TATTAATATTTTTTA
Found at i:3876300 original size:23 final size:23
Alignment explanation
Indices: 3876266--3876310 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
3876256 TAGTAAATTT
*
3876266 AATAATATAAATATTATATAAAA
1 AATAATATAAATATAATATAAAA
*
3876289 AATAAT-TAAAATGTAATATAAA
1 AATAATAT-AAATATAATATAAA
3876311 TATGATATGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 1 0.05
23 18 0.95
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (23 bp):
AATAATATAAATATAATATAAAA
Found at i:3876360 original size:32 final size:32
Alignment explanation
Indices: 3876310--3876392 Score: 96
Period size: 33 Copynumber: 2.5 Consensus size: 32
3876300 TGTAATATAA
* * *
3876310 ATATGATATGAATATATTAATAT-TTTAAAATTT
1 ATATAATATAAAT-TATTAACATATTT-AAATTT
3876343 ATATAATATAAATTATTAACATATTTAAATTT
1 ATATAATATAAATTATTAACATATTTAAATTT
*
3876375 ATATAAATATAAAATATT
1 ATAT-AATATAAATTATT
3876393 TTAAAAATAA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
32 18 0.41
33 26 0.59
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.46
Consensus pattern (32 bp):
ATATAATATAAATTATTAACATATTTAAATTT
Found at i:3876368 original size:34 final size:33
Alignment explanation
Indices: 3876323--3876392 Score: 99
Period size: 32 Copynumber: 2.2 Consensus size: 33
3876313 TGATATGAAT
*
3876323 ATATTAATAT-TTTAAAATTTATAT-AATATAAA
1 ATATTAACATATTT-AAATTTATATAAATATAAA
*
3876355 TTATTAACATATTTAAATTTATATAAATATAAA
1 ATATTAACATATTTAAATTTATATAAATATAAA
3876388 ATATT
1 ATATT
3876393 TTAAAAATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
32 18 0.55
33 15 0.45
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (33 bp):
ATATTAACATATTTAAATTTATATAAATATAAA
Found at i:3876389 original size:17 final size:17
Alignment explanation
Indices: 3876335--3876389 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
3876325 ATTAATATTT
3876335 TAAAATTTATAT-AATA
1 TAAAATTTATATAAATA
3876351 T-AAA-TTAT-TAACATA
1 TAAAATTTATATAA-ATA
*
3876366 TTTAAATTTATATAAATA
1 -TAAAATTTATATAAATA
3876384 TAAAAT
1 TAAAAT
3876390 ATTTTAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 11
0.73 0.02 0.25
Matches are distributed among these distances:
13 1 0.03
14 5 0.16
15 6 0.19
16 2 0.06
17 8 0.25
18 7 0.22
19 3 0.09
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAAATTTATATAAATA
Found at i:3877741 original size:2 final size:2
Alignment explanation
Indices: 3877734--3877788 Score: 69
Period size: 2 Copynumber: 28.5 Consensus size: 2
3877724 AATGGAACCA
* *
3877734 AT AT AT AT GT AT AT A- AT AT AT GT AT AT -T 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
*
3877774 AT AT AT GT AT AT AT A
1 AT AT AT AT AT AT AT A
3877789 AGAAACTGAT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
1 2 0.04
2 43 0.96
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3878136 original size:3 final size:3
Alignment explanation
Indices: 3878128--3878152 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3878118 TTCCATTTCC
3878128 CGA CGA CGA CGA CGA CGA CGA CGA C
1 CGA CGA CGA CGA CGA CGA CGA CGA C
3878153 ACCTTCCGAC
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:0.32, C:0.36, G:0.32, T:0.00
Consensus pattern (3 bp):
CGA
Found at i:3884044 original size:27 final size:27
Alignment explanation
Indices: 3884014--3884076 Score: 94
Period size: 26 Copynumber: 2.4 Consensus size: 27
3884004 TATAATTTTA
*
3884014 TTTAAAATATTTTAT-ATTTATATAAAT
1 TTTAAAATATTTAATAATTTAT-TAAAT
3884041 TTTAAAAT-TTTAATAATTTATTAAAT
1 TTTAAAATATTTAATAATTTATTAAAT
3884067 TTTAAAATAT
1 TTTAAAATAT
3884077 ATATTTATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
26 18 0.55
27 15 0.45
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (27 bp):
TTTAAAATATTTAATAATTTATTAAAT
Found at i:3884067 original size:9 final size:8
Alignment explanation
Indices: 3884014--3884074 Score: 50
Period size: 9 Copynumber: 7.0 Consensus size: 8
3884004 TATAATTTTA
3884014 TTTAAAAT
1 TTTAAAAT
* *
3884022 ATTTTATAT
1 -TTTAAAAT
3884031 TTATATAAAT
1 TT-TA-AAAT
3884041 TTTAAAAT
1 TTTAAAAT
3884049 TTTAATAAT
1 TTTAA-AAT
*
3884058 TTATTAAAT
1 TT-TAAAAT
3884067 TTTAAAAT
1 TTTAAAAT
3884075 ATATATTTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 9
0.74 0.11 0.16
Matches are distributed among these distances:
8 16 0.38
9 19 0.45
10 7 0.17
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (8 bp):
TTTAAAAT
Found at i:3885124 original size:26 final size:25
Alignment explanation
Indices: 3885067--3885124 Score: 73
Period size: 24 Copynumber: 2.3 Consensus size: 25
3885057 ATAAAAGTCA
3885067 CTATTTGTGTTTGTAAAAAATAGTGG
1 CTATTT-TGTTTGTAAAAAATAGTGG
* *
3885093 CT-TTTTGTTTGTCAAAATTAGTGG
1 CTATTTTGTTTGTAAAAAATAGTGG
3885117 CTAATTTT
1 CT-ATTTT
3885125 TATTACAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 19 0.68
25 3 0.11
26 6 0.21
ACGTcount: A:0.26, C:0.07, G:0.19, T:0.48
Consensus pattern (25 bp):
CTATTTTGTTTGTAAAAAATAGTGG
Found at i:3889591 original size:27 final size:27
Alignment explanation
Indices: 3889561--3889636 Score: 89
Period size: 27 Copynumber: 2.8 Consensus size: 27
3889551 AAAGCCACCA
*
3889561 TTTGTGTTTGTCGAAAATGGTGGTTCC
1 TTTGTGTTTGTCAAAAATGGTGGTTCC
* ** *
3889588 TTTGTGTTTATCAAAAATAATAGTTCC
1 TTTGTGTTTGTCAAAAATGGTGGTTCC
* *
3889615 TTTTTGTTTGTAAAAAATGGTG
1 TTTGTGTTTGTCAAAAATGGTG
3889637 ACTTGTTATT
Statistics
Matches: 38, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.25, C:0.08, G:0.21, T:0.46
Consensus pattern (27 bp):
TTTGTGTTTGTCAAAAATGGTGGTTCC
Found at i:3890565 original size:7 final size:7
Alignment explanation
Indices: 3890553--3890582 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
3890543 ATATTGTTTA
3890553 CCTATCC
1 CCTATCC
3890560 CCTATCC
1 CCTATCC
3890567 CCTATCC
1 CCTATCC
3890574 CCTATCC
1 CCTATCC
3890581 CC
1 CC
3890583 CATGTCTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.13, C:0.60, G:0.00, T:0.27
Consensus pattern (7 bp):
CCTATCC
Found at i:3891192 original size:2 final size:2
Alignment explanation
Indices: 3891185--3891221 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3891175 TTTGAGTCGT
3891185 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3891222 TAAATTTAAA
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3891465 original size:18 final size:18
Alignment explanation
Indices: 3891422--3891478 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 18
3891412 ACTCAAATAA
*
3891422 TTATTTAAAAAAT-ATTA
1 TTATTTAAAAAATAATTT
**
3891439 AAATATTAAAAAATAATTT
1 TTAT-TTAAAAAATAATTT
*
3891458 TTATTTAATAAATAATGTT
1 TTATTTAAAAAATAAT-TT
3891477 TT
1 TT
3891479 GGATTGGTCT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
17 2 0.06
18 20 0.65
19 9 0.29
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
TTATTTAAAAAATAATTT
Found at i:3891959 original size:3 final size:3
Alignment explanation
Indices: 3891953--3891986 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
3891943 GTAGTAGTAG
*
3891953 TAA TAA TAA TAA TAA TAA TGA TAA TAA TTAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA
3891987 AACGAAAGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:3892896 original size:18 final size:21
Alignment explanation
Indices: 3892853--3892896 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
3892843 TCACGAAAAG
3892853 AAAATGATATAAAATATATTT
1 AAAATGATATAAAATATATTT
*
3892874 TAAAT-ATATAAAAT-T-TTT
1 AAAATGATATAAAATATATTT
3892892 AAAAT
1 AAAAT
3892897 TTATTTAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 7 0.33
19 1 0.05
20 9 0.43
21 4 0.19
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (21 bp):
AAAATGATATAAAATATATTT
Found at i:3897424 original size:30 final size:31
Alignment explanation
Indices: 3897388--3897448 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
3897378 GCAGTTCCCT
* *
3897388 TTTTTAA-TTATGTAATT-AATAAAATATATA
1 TTTTTAATTTATATAATTGAAAAAAAT-TATA
3897418 TTTTTAATTTATATAATTGAAAAAAATTATA
1 TTTTTAATTTATATAATTGAAAAAAATTATA
3897449 AAATTTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 7 0.26
31 13 0.48
32 7 0.26
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (31 bp):
TTTTTAATTTATATAATTGAAAAAAATTATA
Found at i:3897663 original size:15 final size:16
Alignment explanation
Indices: 3897643--3897672 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3897633 TTAAATAAAT
3897643 ATTATTA-TTTATTTA
1 ATTATTATTTTATTTA
3897658 ATTATTATTTTATTT
1 ATTATTATTTTATTT
3897673 TTTAAAATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
ATTATTATTTTATTTA
Found at i:3898141 original size:19 final size:18
Alignment explanation
Indices: 3898117--3898175 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 18
3898107 TACACGAATG
3898117 TATTAAAATATATATAAAA
1 TATTAAAAT-TATATAAAA
*
3898136 TATTAAAATTAATTATTAAA
1 TATTAAAATT-A-TATAAAA
* *
3898156 TGTAAAAATTTATATAAAA
1 TATTAAAA-TTATATAAAA
3898175 T
1 T
3898176 TATAATATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
18 1 0.03
19 17 0.52
20 13 0.39
21 2 0.06
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.41
Consensus pattern (18 bp):
TATTAAAATTATATAAAA
Found at i:3898351 original size:11 final size:12
Alignment explanation
Indices: 3898335--3898384 Score: 50
Period size: 11 Copynumber: 4.2 Consensus size: 12
3898325 TATTATTATG
3898335 AAATATAA-ATA
1 AAATATAATATA
3898346 AAATATAATATAA
1 AAATATAATAT-A
*
3898359 AAAAATAAT-TA
1 AAATATAATATA
* *
3898370 AGATACAATATA
1 AAATATAATATA
3898382 AAA
1 AAA
3898385 AATACATAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
11 15 0.48
12 7 0.23
13 9 0.29
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (12 bp):
AAATATAATATA
Found at i:3898357 original size:16 final size:15
Alignment explanation
Indices: 3898336--3898365 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
3898326 ATTATTATGA
3898336 AATATAAATAAAATAT
1 AATATAAA-AAAATAT
3898352 AATATAAAAAAATA
1 AATATAAAAAAATA
3898366 ATTAAGATAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
AATATAAAAAAATAT
Found at i:3898366 original size:24 final size:24
Alignment explanation
Indices: 3898339--3898386 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
3898329 ATTATGAAAT
*
3898339 ATAAATAAAATATAATATAAAAAA
1 ATAAATAAAATACAATATAAAAAA
* *
3898363 ATAATTAAGATACAATATAAAAAA
1 ATAAATAAAATACAATATAAAAAA
3898387 TACATAATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (24 bp):
ATAAATAAAATACAATATAAAAAA
Found at i:3899690 original size:19 final size:19
Alignment explanation
Indices: 3899668--3899708 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
3899658 CAATCATCTA
3899668 TAAAAAAA-TATTATTTAAT
1 TAAAAAAATTATT-TTTAAT
*
3899687 TAAAAAAATTATTTTTATT
1 TAAAAAAATTATTTTTAAT
3899706 TAA
1 TAA
3899709 TTTTAACAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TAAAAAAATTATTTTTAAT
Found at i:3899800 original size:12 final size:14
Alignment explanation
Indices: 3899762--3899911 Score: 76
Period size: 14 Copynumber: 10.1 Consensus size: 14
3899752 TTCATCGATC
*
3899762 TATAAATTATAATAA
1 TATAAA-TATAATTA
3899777 TA-AAATTGATAATT-
1 TATAAA-T-ATAATTA
3899791 T-TAAATATAATTA
1 TATAAATATAATTA
3899804 TATAAATATAA-TA
1 TATAAATATAATTA
*
3899817 TATAATATATAAATA
1 TATAA-ATATAATTA
** *
3899832 TATATTTTAAAAATTA
1 TATA-AAT-ATAATTA
3899848 TATAATATATATTATTAA
1 TATAA-ATATA--ATT-A
*
3899866 TATATAA-AAAATTA
1 TATA-AATATAATTA
*
3899880 TATAAATATAAAATAA
1 TATAAATAT--AATTA
*
3899896 TTTAAATATAATTA
1 TATAAATATAATTA
3899910 TA
1 TA
3899912 ATATGATAAA
Statistics
Matches: 105, Mismatches: 14, Indels: 33
0.69 0.09 0.22
Matches are distributed among these distances:
12 6 0.06
13 11 0.10
14 35 0.33
15 19 0.18
16 22 0.21
17 5 0.05
18 6 0.06
19 1 0.01
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.43
Consensus pattern (14 bp):
TATAAATATAATTA
Found at i:3899810 original size:28 final size:27
Alignment explanation
Indices: 3899762--3899929 Score: 84
Period size: 28 Copynumber: 6.2 Consensus size: 27
3899752 TTCATCGATC
*
3899762 TATAAATTATAATAATA-AAATTGATAAT-
1 TATAAA-TATAATTATATAAA-T-ATAATA
*
3899790 TTTAAATATAATTATATAAATATAATA
1 TATAAATATAATTATATAAATATAATA
* * *
3899817 TATAATATATAAATATAT-ATTTTAA-A
1 TATAA-ATATAATTATATAAATATAATA
* * *
3899843 AAT-TATATAA-TATAT-ATTATTAATA
1 TATAAATATAATTATATAAATA-TAATA
3899868 TATAAA-A-AATTATATAAATATAAAATAA
1 TATAAATATAATTATATAAATAT--AAT-A
* * *
3899896 TTTAAATATAATTATAATATGATAAAATA
1 TATAAATATAATTAT-ATA-AATATAATA
3899925 TATAA
1 TATAA
3899930 TATGATACAA
Statistics
Matches: 109, Mismatches: 16, Indels: 29
0.71 0.10 0.19
Matches are distributed among these distances:
23 8 0.07
24 11 0.10
25 10 0.09
26 12 0.11
27 22 0.20
28 25 0.23
29 6 0.06
30 9 0.08
31 3 0.03
32 3 0.03
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (27 bp):
TATAAATATAATTATATAAATATAATA
Found at i:3899825 original size:20 final size:20
Alignment explanation
Indices: 3899795--3899949 Score: 103
Period size: 20 Copynumber: 7.8 Consensus size: 20
3899785 ATAATTTTAA
3899795 ATATAATTATATAAATATAAT
1 ATATAA-TATATAAATATAAT
3899816 ATATAATATATAAATATATATT
1 ATATAATATATAAATATA-A-T
* * *
3899838 TTAAAAATTATATAATATATATT
1 AT-ATAA-TATATAA-ATATAAT
3899861 AT-TAATATATAAA-A-AATT
1 ATATAATATATAAATATAA-T
3899879 ATATAA-ATATAAA-ATAAT
1 ATATAATATATAAATATAAT
*
3899897 -T-TAA-ATATAATTATAAT
1 ATATAATATATAAATATAAT
* *
3899914 ATGATAAAATATATAATATGAT
1 AT-ATAATATATA-AATATAAT
*
3899936 ACA-AATATATAAAT
1 ATATAATATATAAAT
3899950 TATTCAATTT
Statistics
Matches: 109, Mismatches: 11, Indels: 30
0.73 0.07 0.20
Matches are distributed among these distances:
16 9 0.08
17 7 0.06
18 14 0.13
19 9 0.08
20 29 0.27
21 15 0.14
22 9 0.08
23 5 0.05
24 7 0.06
25 5 0.05
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (20 bp):
ATATAATATATAAATATAAT
Found at i:3899851 original size:38 final size:37
Alignment explanation
Indices: 3899809--3899946 Score: 110
Period size: 36 Copynumber: 3.7 Consensus size: 37
3899799 AATTATATAA
3899809 ATATAATATATAATATATAAATATATATTTTAAAAATT
1 ATATAATATATAATATATAAATATATA-TTTAAAAATT
*
3899847 ATATAATATAT-AT-TATTAATATATA---AAAAATT
1 ATATAATATATAATATATAAATATATATTTAAAAATT
* * * *
3899879 ATATAAATATAAAATAATTTAAATATA-A-TTATAATATG
1 ATAT-AATATATAAT-ATATAAATATATATTTA-AAAATT
*
3899917 ATAAAATATATAATATGATACAAATATATA
1 ATATAATATATAATAT-AT--AAATATATA
3899947 AATTATTCAA
Statistics
Matches: 80, Mismatches: 9, Indels: 20
0.73 0.08 0.18
Matches are distributed among these distances:
32 11 0.14
33 6 0.08
34 2 0.03
35 1 0.01
36 21 0.26
37 13 0.16
38 18 0.22
39 7 0.09
40 1 0.01
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (37 bp):
ATATAATATATAATATATAAATATATATTTAAAAATT
Found at i:3899943 original size:18 final size:17
Alignment explanation
Indices: 3899908--3899947 Score: 71
Period size: 17 Copynumber: 2.3 Consensus size: 17
3899898 TAAATATAAT
3899908 TATAATATGATAAAATA
1 TATAATATGATAAAATA
3899925 TATAATATGATACAAATA
1 TATAATATGATA-AAATA
3899943 TATAA
1 TATAA
3899948 ATTATTCAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 12 0.55
18 10 0.45
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.35
Consensus pattern (17 bp):
TATAATATGATAAAATA
Found at i:3899949 original size:47 final size:44
Alignment explanation
Indices: 3899802--3899949 Score: 142
Period size: 47 Copynumber: 3.2 Consensus size: 44
3899792 TAAATATAAT
* *
3899802 TATATAAATATAATATATAATATAT-AAATATATATTTTA-AAAA
1 TATATAAATATAAT-TATAATATATAAAATATATAATATATAAAA
3899845 T-TATATAATATATATTATTAATATATAAAAAATTATATAA-ATATAAAA
1 TATATA-AATATA-ATTA-TAATATAT--AAAA-TATATAATATATAAAA
*
3899893 TAATTTAAATATAATTATAATATGATAAAATATATAATATGATACAAA
1 T-ATATAAATATAATTATAATAT-ATAAAATATATAATAT-ATA-AAA
3899941 TATATAAAT
1 TATATAAAT
3899950 TATTCAATTT
Statistics
Matches: 87, Mismatches: 4, Indels: 24
0.76 0.03 0.21
Matches are distributed among these distances:
42 4 0.05
43 9 0.10
44 10 0.11
45 7 0.08
46 6 0.07
47 21 0.24
48 21 0.24
49 6 0.07
50 3 0.03
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (44 bp):
TATATAAATATAATTATAATATATAAAATATATAATATATAAAA
Found at i:3901272 original size:21 final size:21
Alignment explanation
Indices: 3901248--3901288 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
3901238 TAAATTAATC
3901248 CAAAATTTTATTTTATATTAT
1 CAAAATTTTATTTTATATTAT
3901269 CAAAATTTTATTTTATATTA
1 CAAAATTTTATTTTATATTA
3901289 ATATTATGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (21 bp):
CAAAATTTTATTTTATATTAT
Found at i:3901826 original size:22 final size:23
Alignment explanation
Indices: 3901774--3901831 Score: 68
Period size: 22 Copynumber: 2.6 Consensus size: 23
3901764 TTGTGTATAT
3901774 TTATA-TATGTTTTATATTCTTG
1 TTATATTATGTTTTATATTCTTG
*
3901796 TTATATTATGTTTTA-ATT-TTT
1 TTATATTATGTTTTATATTCTTG
*
3901817 TTCATATTATTTTTT
1 TT-ATATTATGTTTT
3901832 GTATAATATA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 4 0.12
22 19 0.59
23 9 0.28
ACGTcount: A:0.22, C:0.03, G:0.05, T:0.69
Consensus pattern (23 bp):
TTATATTATGTTTTATATTCTTG
Found at i:3902627 original size:17 final size:16
Alignment explanation
Indices: 3902605--3902659 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 16
3902595 TATCTGGGTA
3902605 AAATTTAATTTTATATT
1 AAATTTAATTTTAT-TT
3902622 AAATTT-A-TTTATTT
1 AAATTTAATTTTATTT
*
3902636 AATTTTGAATTTTAATTT
1 AAATTT-AATTTT-ATTT
3902654 ATAATT
1 A-AATT
3902660 AGTTTATAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
14 7 0.23
15 5 0.16
16 2 0.06
17 9 0.29
18 5 0.16
19 3 0.10
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (16 bp):
AAATTTAATTTTATTT
Found at i:3903179 original size:30 final size:29
Alignment explanation
Indices: 3903145--3903204 Score: 68
Period size: 30 Copynumber: 2.0 Consensus size: 29
3903135 ATCAAATATT
*
3903145 TAATAAAGATCATATAAAAA-TAAAATAAAA
1 TAATAAA-A-CATAAAAAAATTAAAATAAAA
*
3903175 TAATATAACATAAAAAAATTTAAAATAAAA
1 TAATAAAACATAAAAAAA-TTAAAATAAAA
3903205 ATTATTAACA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
28 9 0.35
29 1 0.04
30 16 0.62
ACGTcount: A:0.70, C:0.03, G:0.02, T:0.25
Consensus pattern (29 bp):
TAATAAAACATAAAAAAATTAAAATAAAA
Found at i:3903187 original size:15 final size:15
Alignment explanation
Indices: 3903160--3903205 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
3903150 AAGATCATAT
3903160 AAAA-ATAAAATAAA
1 AAAATATAAAATAAA
* *
3903174 ATAATATAACATAAA
1 AAAATATAAAATAAA
*
3903189 AAAATTTAAAATAAA
1 AAAATATAAAATAAA
3903204 AA
1 AA
3903206 TTATTAACAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
14 3 0.12
15 23 0.88
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (15 bp):
AAAATATAAAATAAA
Found at i:3903259 original size:5 final size:5
Alignment explanation
Indices: 3903251--3903306 Score: 50
Period size: 5 Copynumber: 12.0 Consensus size: 5
3903241 TATAATAAAC
* *
3903251 ATATT ATATT ATATT -TATT A-AAT ATATA AT-TT ATATT CATATT ATATT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT -ATATT ATATT
3903299 -T-TT ATATT
1 ATATT ATATT
3903307 TTTTTTAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
3 2 0.05
4 12 0.29
5 22 0.54
6 5 0.12
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (5 bp):
ATATT
Found at i:3903260 original size:23 final size:23
Alignment explanation
Indices: 3903232--3903286 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
3903222 ATTTTTTAAA
3903232 AATATTATATATAATAAACATAT
1 AATATTATATATAATAAACATAT
* * * *
3903255 TATATTATATTTATTAAATATAT
1 AATATTATATATAATAAACATAT
3903278 AAT-TTATAT
1 AATATTATAT
3903287 TCATATTATA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 6 0.22
23 21 0.78
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (23 bp):
AATATTATATATAATAAACATAT
Found at i:3903564 original size:22 final size:21
Alignment explanation
Indices: 3903500--3903596 Score: 81
Period size: 22 Copynumber: 4.3 Consensus size: 21
3903490 TTAAATGTAA
3903500 ATTAAATTTAAATAATTTTT-T
1 ATTAAATTTAAAT-ATTTTTAT
** *
3903521 ATT-TTTTTAAAAATATTTTAT
1 ATTAAATTTAAATAT-TTTTAT
3903542 ATTAAAATTTAAATATTTTTAT
1 ATT-AAATTTAAATATTTTTAT
3903564 AATTAAATTTAAATAAATTTTTATT
1 -ATTAAATTTAAAT--ATTTTTA-T
3903589 ATTTAAAT
1 A-TTAAAT
3903597 AATAATTTAA
Statistics
Matches: 61, Mismatches: 6, Indels: 14
0.75 0.07 0.17
Matches are distributed among these distances:
19 2 0.03
20 10 0.16
21 7 0.11
22 16 0.26
23 11 0.18
24 8 0.13
25 7 0.11
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
ATTAAATTTAAATATTTTTAT
Found at i:3903616 original size:22 final size:22
Alignment explanation
Indices: 3903602--3903647 Score: 62
Period size: 20 Copynumber: 2.2 Consensus size: 22
3903592 TAAATAATAA
3903602 TTTAA-AATAAATTAAATTAAT
1 TTTAATAATAAATTAAATTAAT
*
3903623 TTTAATAATAAA--AAATTTAT
1 TTTAATAATAAATTAAATTAAT
3903643 TTTAA
1 TTTAA
3903648 ACTCGATTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 12 0.52
21 5 0.22
22 6 0.26
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
TTTAATAATAAATTAAATTAAT
Found at i:3903625 original size:65 final size:65
Alignment explanation
Indices: 3903499--3903631 Score: 164
Period size: 65 Copynumber: 2.0 Consensus size: 65
3903489 TTTAAATGTA
* * * * * *
3903499 AATTAAATTTAAATAATTTTTTATTTTTTTAAAAATATTTTATATTAAAATTTAAATATTTTTAT
1 AATTAAATTTAAATAAATTTTTATTTATTTAAAAATAATTTAAAATAAAATTTAAATATTTTAAT
3903564 AATTAAATTTAAATAAATTTTTA-TTATTTAAATAATAATTTAAAAT-AAA-TTAAATTAATTTT
1 AATTAAATTTAAATAAATTTTTATTTATTTAAA-AATAATTTAAAATAAAATTTAAA-T-ATTTT
3903626 AAT
63 AAT
3903629 AAT
1 AAT
3903632 AAAAAATTTA
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
63 5 0.08
64 12 0.20
65 42 0.71
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (65 bp):
AATTAAATTTAAATAAATTTTTATTTATTTAAAAATAATTTAAAATAAAATTTAAATATTTTAAT
Found at i:3903984 original size:11 final size:11
Alignment explanation
Indices: 3903936--3903986 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
3903926 ATATTAAATA
3903936 TTTAAA-ATTT
1 TTTAAATATTT
3903946 TTTAAATTATATT
1 TTTAAA-TAT-TT
* *
3903959 TTTATTATACTT
1 TTTA-AATATTT
3903971 TTTAAATATTT
1 TTTAAATATTT
3903982 TTTAA
1 TTTAA
3903987 CTTAAATTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
10 6 0.18
11 10 0.30
12 8 0.24
13 8 0.24
14 1 0.03
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (11 bp):
TTTAAATATTT
Found at i:3904738 original size:24 final size:26
Alignment explanation
Indices: 3904707--3904792 Score: 74
Period size: 25 Copynumber: 3.4 Consensus size: 26
3904697 TAAATTTTTA
3904707 AAAT-TATAAA-TTTTAAAA-AAATT
1 AAATATATAAATTTTTAAAATAAATT
3904730 AAATATATAATATTTTTAAAATAAATT
1 AAATATATAA-ATTTTTAAAATAAATT
* * * * *
3904757 AATTAAATAAAATTAT-AAGTAAA-T
1 AAATATATAAATTTTTAAAATAAATT
3904781 AAATAATATAAA
1 AAAT-ATATAAA
3904793 ATAATATTTA
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
23 4 0.08
24 9 0.18
25 13 0.25
26 12 0.24
27 13 0.25
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (26 bp):
AAATATATAAATTTTTAAAATAAATT
Found at i:3905402 original size:17 final size:18
Alignment explanation
Indices: 3905374--3905409 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
3905364 TACGATGGTC
3905374 ATCAATTGCGTAATTAAG
1 ATCAATTGCGTAATTAAG
3905392 ATCAA-TGCGTAATTAAG
1 ATCAATTGCGTAATTAAG
3905409 A
1 A
3905410 CACTGCACGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.42, C:0.11, G:0.17, T:0.31
Consensus pattern (18 bp):
ATCAATTGCGTAATTAAG
Found at i:3906282 original size:20 final size:20
Alignment explanation
Indices: 3906242--3906288 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
3906232 ATGATAATTT
* *
3906242 TAAATATAATATAAATTTAA
1 TAAATATAAAATAAATATAA
*
3906262 TAAATATAAAATTAATATAA
1 TAAATATAAAATAAATATAA
3906282 TAAATAT
1 TAAATAT
3906289 GATAAATATG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
TAAATATAAAATAAATATAA
Found at i:3906771 original size:18 final size:18
Alignment explanation
Indices: 3906748--3906788 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
3906738 TAAATTGAGT
3906748 AAATTTAAATTAAAAATA
1 AAATTTAAATTAAAAATA
* *
3906766 AAATTTAAATTAATAATT
1 AAATTTAAATTAAAAATA
3906784 AAATT
1 AAATT
3906789 AATAATTATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
AAATTTAAATTAAAAATA
Found at i:3906785 original size:12 final size:12
Alignment explanation
Indices: 3906770--3906796 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
3906760 AAAATAAAAT
3906770 TTAAATTAATAA
1 TTAAATTAATAA
3906782 TTAAATTAATAA
1 TTAAATTAATAA
3906794 TTA
1 TTA
3906797 TGAATATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TTAAATTAATAA
Found at i:3907181 original size:25 final size:25
Alignment explanation
Indices: 3907122--3907190 Score: 65
Period size: 23 Copynumber: 2.9 Consensus size: 25
3907112 AAATTTAATA
*
3907122 ATTTAATAAT-TTATATTATTTTTAT
1 ATTT-ATAATATTATATTATATTTAT
* *
3907147 A--AATATTATTATATTATATTTAT
1 ATTTATAATATTATATTATATTTAT
*
3907170 ATTTATAATATTTTA-TATATT
1 ATTTATAATATTATATTATATT
3907191 AATAAATTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
22 4 0.11
23 15 0.43
24 6 0.17
25 10 0.29
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (25 bp):
ATTTATAATATTATATTATATTTAT
Found at i:3907188 original size:29 final size:28
Alignment explanation
Indices: 3907132--3907230 Score: 80
Period size: 29 Copynumber: 3.5 Consensus size: 28
3907122 ATTTAATAAT
*
3907132 TTATATTATTTTTATAAATATTATTATA
1 TTATATTATATTTATAAATATTATTATA
3907160 TTATATTTATATTTAT-AATATT-TTATA
1 TTATA-TTATATTTATAAATATTATTATA
* * * *
3907187 -TATTAATAAATTT-TAAAATGTTGTTATA
1 TTA-TATTATATTTAT-AAATATTATTATA
*
3907215 CTCATATTATATTTAT
1 -TTATATTATATTTAT
3907231 TTTATTGTTA
Statistics
Matches: 56, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
25 1 0.02
26 8 0.14
27 12 0.21
28 16 0.29
29 17 0.30
30 2 0.04
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (28 bp):
TTATATTATATTTATAAATATTATTATA
Found at i:3910714 original size:2 final size:2
Alignment explanation
Indices: 3910704--3910738 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
3910694 CTCTCTCTCT
*
3910704 CA CA TA CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
3910739 GTATATCTAA
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:0.49, C:0.49, G:0.00, T:0.03
Consensus pattern (2 bp):
CA
Found at i:3911519 original size:3 final size:3
Alignment explanation
Indices: 3911511--3911551 Score: 64
Period size: 3 Copynumber: 13.0 Consensus size: 3
3911501 TGTATCAGTG
3911511 ATT ATT ATT ATT ATT ATT ATT ATT ATTT ATT ATTT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT A-TT ATT ATT
3911552 TTACAAAGGA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
3 30 0.83
4 6 0.17
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:3912226 original size:12 final size:12
Alignment explanation
Indices: 3912209--3912235 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
3912199 AATTATATAA
3912209 TTAAATTAAATT
1 TTAAATTAAATT
3912221 TTAAATTAAATT
1 TTAAATTAAATT
3912233 TTA
1 TTA
3912236 TCTTCTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TTAAATTAAATT
Found at i:3916478 original size:16 final size:16
Alignment explanation
Indices: 3916457--3916487 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
3916447 ATTTTTTGAC
3916457 GAAATTACTGTACATG
1 GAAATTACTGTACATG
3916473 GAAATTACTGTACAT
1 GAAATTACTGTACAT
3916488 CAAATAGACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (16 bp):
GAAATTACTGTACATG
Found at i:3918660 original size:15 final size:16
Alignment explanation
Indices: 3918640--3918715 Score: 50
Period size: 18 Copynumber: 4.7 Consensus size: 16
3918630 CTAATTAATT
*
3918640 TTAAAATTTAAA-AAA
1 TTAAAAATTAAATAAA
3918655 TTAAAAATTAAATAAA
1 TTAAAAATTAAATAAA
* * *
3918671 TCGATTAAATTAATTAAA
1 T-TA-AAAATTAAATAAA
*
3918689 TTAAATTTATTAAA-AAA
1 TTAAA--AATTAAATAAA
3918706 TT-AAAATTAA
1 TTAAAAATTAA
3918716 TTTAGATCGA
Statistics
Matches: 47, Mismatches: 9, Indels: 11
0.70 0.13 0.16
Matches are distributed among these distances:
14 5 0.11
15 11 0.23
16 7 0.15
17 7 0.15
18 17 0.36
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.37
Consensus pattern (16 bp):
TTAAAAATTAAATAAA
Found at i:3918707 original size:22 final size:22
Alignment explanation
Indices: 3918657--3918719 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
3918647 TTAAAAAATT
**
3918657 AAAAATTAAA-TAAATCGATTA
1 AAAAATTAAATTAAATTTATTA
*
3918678 AATTAATTAAATTAAATTTATTA
1 AA-AAATTAAATTAAATTTATTA
3918701 AAAAATTAAAATT-AATTTA
1 AAAAATT-AAATTAAATTTA
3918720 GATCGATTGA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
21 2 0.06
22 17 0.49
23 16 0.46
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (22 bp):
AAAAATTAAATTAAATTTATTA
Found at i:3919040 original size:109 final size:109
Alignment explanation
Indices: 3918904--3919114 Score: 296
Period size: 109 Copynumber: 1.9 Consensus size: 109
3918894 TTTGTTCGTT
* * * * * * **
3918904 TATTAAGTTTAAAAACTAATAATTTACCAAATTAATCAAAAAACTGTTTTTCATAGTTAATTAAT
1 TATTAAGTTTAAAAACCAACAACTTACCAAACTAAACAAAAAACTATTTTTCATAACTAATTAAT
*
3918969 TTTAAACTAAATAAGTCAAATTAAATTAATTAAATTTGATCGAA
66 TTTAAACTAAATAAGTCAAATCAAATTAATTAAATTTGATCGAA
* *
3919013 TATTAAGTTTAAAAACCAACAACTTACCAAACTAAACCAAAAATTATTTTTCATAACTAATTAAT
1 TATTAAGTTTAAAAACCAACAACTTACCAAACTAAACAAAAAACTATTTTTCATAACTAATTAAT
* * *
3919078 TTTAAATTAAATAATTTAAATCAAATTAATTAAATTT
66 TTTAAACTAAATAAGTCAAATCAAATTAATTAAATTT
3919115 AATTAAATTA
Statistics
Matches: 88, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
109 88 1.00
ACGTcount: A:0.49, C:0.10, G:0.03, T:0.38
Consensus pattern (109 bp):
TATTAAGTTTAAAAACCAACAACTTACCAAACTAAACAAAAAACTATTTTTCATAACTAATTAAT
TTTAAACTAAATAAGTCAAATCAAATTAATTAAATTTGATCGAA
Found at i:3919089 original size:5 final size:5
Alignment explanation
Indices: 3919079--3919125 Score: 53
Period size: 5 Copynumber: 9.8 Consensus size: 5
3919069 CTAATTAATT
* * *
3919079 TTAAA TTAAA -TAAT TTAAA TCAAA TT-AA TTAAA TTTAA TTAAA TTAA
1 TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTAA
3919126 TTATTAAATC
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
4 7 0.21
5 27 0.79
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (5 bp):
TTAAA
Found at i:3919116 original size:10 final size:9
Alignment explanation
Indices: 3919079--3919128 Score: 55
Period size: 9 Copynumber: 5.3 Consensus size: 9
3919069 CTAATTAATT
3919079 TTAAATTAA
1 TTAAATTAA
* *
3919088 ATAATTTAAA
1 TTAAATT-AA
*
3919098 TCAAATTAA
1 TTAAATTAA
3919107 TTAAATTTAA
1 TTAAA-TTAA
3919117 TTAAATTAA
1 TTAAATTAA
3919126 TTA
1 TTA
3919129 TTAAATCGGC
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
9 18 0.55
10 15 0.45
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (9 bp):
TTAAATTAA
Found at i:3919126 original size:19 final size:20
Alignment explanation
Indices: 3919079--3919128 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
3919069 CTAATTAATT
*
3919079 TTAAATTAAAT-AATTTAAA
1 TTAAATTAATTAAATTTAAA
*
3919098 TCAAATTAATTAAATTT-AA
1 TTAAATTAATTAAATTTAAA
3919117 TTAAATTAATTA
1 TTAAATTAATTA
3919129 TTAAATCGGC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 22 0.81
20 5 0.19
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (20 bp):
TTAAATTAATTAAATTTAAA
Found at i:3919127 original size:14 final size:15
Alignment explanation
Indices: 3919071--3919125 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 15
3919061 TTTCATAACT
3919071 AATTAATTTTAAATTA
1 AATTAA-TTTAAATTA
*
3919087 AA-TAATTTAAATCA
1 AATTAATTTAAATTA
*
3919101 AATTAA-TTAAATTT
1 AATTAATTTAAATTA
*
3919115 AATTAAATTAA
1 AATTAATTTAA
3919126 TTATTAAATC
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
14 22 0.65
15 10 0.29
16 2 0.06
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAATTTAAATTA
Found at i:3919273 original size:19 final size:18
Alignment explanation
Indices: 3919249--3919307 Score: 63
Period size: 17 Copynumber: 3.4 Consensus size: 18
3919239 AGTTTAAATA
3919249 TAAATATAATATAAATTAT
1 TAAATATAATATAAATT-T
*
3919268 TAAATAT--TTTAAATTT
1 TAAATATAATATAAATTT
3919284 TAAATATACATAT-AA-TT
1 TAAATATA-ATATAAATTT
3919301 TAAATAT
1 TAAATAT
3919308 TAAATATATC
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
16 8 0.23
17 16 0.46
18 2 0.06
19 9 0.26
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (18 bp):
TAAATATAATATAAATTT
Found at i:3919280 original size:17 final size:17
Alignment explanation
Indices: 3919231--3919290 Score: 56
Period size: 17 Copynumber: 3.6 Consensus size: 17
3919221 ATATATTTTT
*
3919231 TTATT-AATAGTTTAAA
1 TTATTAAATATTTTAAA
*
3919247 -TA-TAAATATAATATAAA
1 TTATTAAATAT--TTTAAA
3919264 TTATTAAATATTTTAAA
1 TTATTAAATATTTTAAA
3919281 TT-TTAAATAT
1 TTATTAAATAT
3919291 ACATATAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
14 1 0.03
15 6 0.17
16 8 0.22
17 12 0.33
18 2 0.06
19 7 0.19
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (17 bp):
TTATTAAATATTTTAAA
Found at i:3919302 original size:24 final size:26
Alignment explanation
Indices: 3919275--3919342 Score: 90
Period size: 24 Copynumber: 2.8 Consensus size: 26
3919265 TATTAAATAT
*
3919275 TTTAAATTTTAAATATA-CATAT-AA
1 TTTAAATTTTAAATATATCACATCAA
*
3919299 TTTAAATATTAAATATATCACATCAA
1 TTTAAATTTTAAATATATCACATCAA
3919325 -TTAAA-TTTAAATATATCA
1 TTTAAATTTTAAATATATCA
3919343 AAATTATTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
24 28 0.72
25 9 0.23
26 2 0.05
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (26 bp):
TTTAAATTTTAAATATATCACATCAA
Found at i:3919638 original size:16 final size:17
Alignment explanation
Indices: 3919617--3919650 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
3919607 TTAACTTTTT
*
3919617 TATTTTTCAAT-TAAAA
1 TATTTTTAAATATAAAA
3919633 TATTTTTAAATATAAAA
1 TATTTTTAAATATAAAA
3919650 T
1 T
3919651 TATCTTTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (17 bp):
TATTTTTAAATATAAAA
Found at i:3919853 original size:12 final size:11
Alignment explanation
Indices: 3919808--3919855 Score: 51
Period size: 11 Copynumber: 4.1 Consensus size: 11
3919798 TAAAAAATAT
*
3919808 TTTTAATTTAT
1 TTTTAATTTAA
3919819 TTTTAATTTAA
1 TTTTAATTTAA
*
3919830 TTATATATATTAA
1 TTTTA-AT-TTAA
3919843 TTTTAATATTAA
1 TTTTAAT-TTAA
3919855 T
1 T
3919856 AAATTATATT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
11 14 0.44
12 10 0.31
13 8 0.25
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TTTTAATTTAA
Found at i:3919854 original size:25 final size:24
Alignment explanation
Indices: 3919819--3919881 Score: 69
Period size: 24 Copynumber: 2.7 Consensus size: 24
3919809 TTTAATTTAT
*
3919819 TTTTAATTTAAT-TATATATATTAA
1 TTTTAATTTAATAAAT-TATATTAA
3919843 TTTTAATATTAATAAATTATATT-A
1 TTTTAAT-TTAATAAATTATATTAA
*
3919867 TTTTTATTTAA-AAAT
1 TTTTAATTTAATAAAT
3919882 AAATAAATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
22 4 0.11
23 4 0.11
24 14 0.40
25 11 0.31
26 2 0.06
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
TTTTAATTTAATAAATTATATTAA
Found at i:3919891 original size:25 final size:27
Alignment explanation
Indices: 3919853--3919905 Score: 74
Period size: 25 Copynumber: 2.0 Consensus size: 27
3919843 TTTTAATATT
* *
3919853 AATAAATTATATTATTTTTATT-TAAA
1 AATAAATTAAATTATTATTATTATAAA
3919879 AATAAA-TAAATTATTATTATTATAAA
1 AATAAATTAAATTATTATTATTATAAA
3919905 A
1 A
3919906 GTTTTGAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 13 0.54
26 11 0.46
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (27 bp):
AATAAATTAAATTATTATTATTATAAA
Found at i:3920187 original size:37 final size:38
Alignment explanation
Indices: 3920145--3920238 Score: 113
Period size: 37 Copynumber: 2.5 Consensus size: 38
3920135 AATTTTTTTA
* *
3920145 AATTTAATTAATAATTAAATTAAAA-ATAAGTT--TAAT
1 AATTTAA-TAGTAATTAAATTAAAATATAACTTAATAAT
*
3920181 ATATTTAATATGTACTTAAATTAAAATATAACTTAATAAT
1 A-ATTTAATA-GTAATTAAATTAAAATATAACTTAATAAT
3920221 AATTTAATAGTAATTAAA
1 AATTTAATAGTAATTAAA
3920239 GATAATTTTA
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
36 3 0.06
37 19 0.39
38 14 0.29
39 8 0.16
40 5 0.10
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.41
Consensus pattern (38 bp):
AATTTAATAGTAATTAAATTAAAATATAACTTAATAAT
Done.