Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007992.1 Hibiscus syriacus cultivar Beakdansim tig00110442_pilon, whole genome shotgun sequence
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: 1314873
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 5
Found at i:1158676 original size:16 final size:16
Alignment explanation
Indices: 1158657--1158709 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 16
1158647 GTTGTAGTTG
*
1158657 AATTTGTTTTGGATTA
1 AATTTGTTTTCGATTA
* *
1158673 AATTTGTTTTCAATTG
1 AATTTGTTTTCGATTA
*
1158689 AATTTGTTTTTGATTA
1 AATTTGTTTTCGATTA
*
1158705 CATTT
1 AATTT
1158710 TAAAACAAGA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.25, C:0.04, G:0.13, T:0.58
Consensus pattern (16 bp):
AATTTGTTTTCGATTA
Found at i:1159066 original size:96 final size:96
Alignment explanation
Indices: 1158893--1159070 Score: 250
Period size: 96 Copynumber: 1.9 Consensus size: 96
1158883 AAAGAACGAA
* * * * * *
1158893 TCCAAGGCCACAACCACCTATACAAGGCTACATTATTAGATGGATTCCTACTCCCACTGTCCATA
1 TCCAAGGCCACAACCACCTATACAAGGCTAAACTATTAGATGGATGCCCACCCCCACTGTCCACA
*
1158958 TGATTCAAGATTCTTTTTCCAACCGATCTTC
66 TGAGTCAAGATTCTTTTTCCAACCGATCTTC
* *
1158989 TCCAAGGCCAGAACCACCT-TCACAAGGCTAAACTATTAGATGGATGCCCACCCCCACTGTTCAC
1 TCCAAGGCCACAACCACCTAT-ACAAGGCTAAACTATTAGATGGATGCCCACCCCCACTGTCCAC
*
1159053 ATGAGTCAGGATTCTTTT
65 ATGAGTCAAGATTCTTTT
1159071 ACCAGCCAAT
Statistics
Matches: 71, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
95 1 0.01
96 70 0.99
ACGTcount: A:0.28, C:0.30, G:0.14, T:0.28
Consensus pattern (96 bp):
TCCAAGGCCACAACCACCTATACAAGGCTAAACTATTAGATGGATGCCCACCCCCACTGTCCACA
TGAGTCAAGATTCTTTTTCCAACCGATCTTC
Found at i:1166498 original size:11 final size:11
Alignment explanation
Indices: 1166482--1166511 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
1166472 TAAAGAGAAC
1166482 TAAACTAAATA
1 TAAACTAAATA
1166493 TAAACTAAATA
1 TAAACTAAATA
1166504 TAAACTAA
1 TAAACTAA
1166512 TTTCCATGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.63, C:0.10, G:0.00, T:0.27
Consensus pattern (11 bp):
TAAACTAAATA
Found at i:1180373 original size:15 final size:15
Alignment explanation
Indices: 1180353--1180388 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
1180343 ATGCTTGGTT
*
1180353 TCAGCTTTCACTGTG
1 TCAGCTTTCACTATG
1180368 TCAGCTTTCACTATG
1 TCAGCTTTCACTATG
1180383 TCAGCT
1 TCAGCT
1180389 CCAGTATCAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.17, C:0.28, G:0.17, T:0.39
Consensus pattern (15 bp):
TCAGCTTTCACTATG
Found at i:1180927 original size:33 final size:33
Alignment explanation
Indices: 1180885--1180952 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
1180875 AGTGCAATGA
1180885 TTAGTGAAGGGAAATAAAGATAACCACTAGCCT
1 TTAGTGAAGGGAAATAAAGATAACCACTAGCCT
1180918 TTAGTGAAGGGAAATAAAGATAACCACTAGCCT
1 TTAGTGAAGGGAAATAAAGATAACCACTAGCCT
1180951 TT
1 TT
1180953 TGGCTATAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.41, C:0.15, G:0.21, T:0.24
Consensus pattern (33 bp):
TTAGTGAAGGGAAATAAAGATAACCACTAGCCT
Found at i:1203526 original size:29 final size:29
Alignment explanation
Indices: 1203484--1203554 Score: 133
Period size: 29 Copynumber: 2.4 Consensus size: 29
1203474 GTTATATCAT
*
1203484 TTATACCACTGAACTTTAAGTTTTACAAA
1 TTATAACACTGAACTTTAAGTTTTACAAA
1203513 TTATAACACTGAACTTTAAGTTTTACAAA
1 TTATAACACTGAACTTTAAGTTTTACAAA
1203542 TTATAACACTGAA
1 TTATAACACTGAA
1203555 ATTTGGTTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (29 bp):
TTATAACACTGAACTTTAAGTTTTACAAA
Found at i:1206524 original size:77 final size:79
Alignment explanation
Indices: 1206439--1206587 Score: 205
Period size: 77 Copynumber: 1.9 Consensus size: 79
1206429 TTAATAAATT
* ***
1206439 TCTTATTTAATTAATT-CAAATTAAATATACATT-AAAGACTTATAATTTGAATTACAATC-TTT
1 TCTTATTTAATT-ATTCCAAATTAAATATAAATTAAAAGACTTATAATCAAAATTACAATCTTTT
1206501 AATGTTTATTTAAAA
65 AATGTTTATTTAAAA
* * *
1206516 TCTTATTTAATTATTCCAAATTAAATATAAATTAAAAGAGTTGTAATCAAAATTACATTCTTTTA
1 TCTTATTTAATTATTCCAAATTAAATATAAATTAAAAGACTTATAATCAAAATTACAATCTTTTA
1206581 ATGTTTA
66 ATGTTTA
1206588 CTTACTTTAT
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
76 3 0.05
77 28 0.45
78 20 0.32
79 11 0.18
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.45
Consensus pattern (79 bp):
TCTTATTTAATTATTCCAAATTAAATATAAATTAAAAGACTTATAATCAAAATTACAATCTTTTA
ATGTTTATTTAAAA
Found at i:1208724 original size:35 final size:35
Alignment explanation
Indices: 1208683--1208761 Score: 131
Period size: 35 Copynumber: 2.3 Consensus size: 35
1208673 ATATAGTACA
*
1208683 TATATAGTATATAGTTTTCATATTAAATGGTATAG
1 TATATAGTATATAGTTTTCATATTAAATCGTATAG
*
1208718 TATATAGTATATAGTTTTCATATTAAATCGTTTAG
1 TATATAGTATATAGTTTTCATATTAAATCGTATAG
*
1208753 CATATAGTA
1 TATATAGTA
1208762 GTACATATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.37, C:0.05, G:0.13, T:0.46
Consensus pattern (35 bp):
TATATAGTATATAGTTTTCATATTAAATCGTATAG
Found at i:1208841 original size:16 final size:16
Alignment explanation
Indices: 1208820--1208852 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1208810 GTGTATCACA
1208820 TTTTCATATTACATAG
1 TTTTCATATTACATAG
*
1208836 TTTTCATATTATATAG
1 TTTTCATATTACATAG
1208852 T
1 T
1208853 CCATATTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.30, C:0.09, G:0.06, T:0.55
Consensus pattern (16 bp):
TTTTCATATTACATAG
Found at i:1217285 original size:15 final size:14
Alignment explanation
Indices: 1217246--1217272 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1217236 CAGGGAATAT
1217246 TCCAAGTCAACTCA
1 TCCAAGTCAACTCA
1217260 TCCAAGTCAACTC
1 TCCAAGTCAACTC
1217273 TATCTGAGTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.37, G:0.07, T:0.22
Consensus pattern (14 bp):
TCCAAGTCAACTCA
Found at i:1217352 original size:14 final size:13
Alignment explanation
Indices: 1217314--1217356 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
1217304 CTGAATCAAC
*
1217314 CCATTGACTTTAA
1 CCATTGACTTTGA
*
1217327 CCATTAACTTTGA
1 CCATTGACTTTGA
1217340 CACATTGACTTTGA
1 C-CATTGACTTTGA
1217354 CCA
1 CCA
1217357 AAAATGGAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
13 14 0.54
14 12 0.46
ACGTcount: A:0.30, C:0.26, G:0.09, T:0.35
Consensus pattern (13 bp):
CCATTGACTTTGA
Found at i:1220800 original size:14 final size:14
Alignment explanation
Indices: 1220781--1220807 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1220771 AGTTAACTCG
1220781 GTCTGAGTCAACCA
1 GTCTGAGTCAACCA
1220795 GTCTGAGTCAACC
1 GTCTGAGTCAACC
1220808 CGTTGACTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.30, G:0.22, T:0.22
Consensus pattern (14 bp):
GTCTGAGTCAACCA
Found at i:1221828 original size:26 final size:26
Alignment explanation
Indices: 1221790--1221845 Score: 87
Period size: 27 Copynumber: 2.2 Consensus size: 26
1221780 GGATTTATAG
1221790 AAATACCCTAAAGTG-TAAATGACCA
1 AAATACCCTAAAGTGTTAAATGACCA
*
1221815 AAATACCCCTAAAGTGTTAAATGACCT
1 AAATA-CCCTAAAGTGTTAAATGACCA
1221842 AAAT
1 AAAT
1221846 TAACTCCAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
25 5 0.18
26 10 0.36
27 13 0.46
ACGTcount: A:0.46, C:0.20, G:0.11, T:0.23
Consensus pattern (26 bp):
AAATACCCTAAAGTGTTAAATGACCA
Found at i:1228003 original size:20 final size:19
Alignment explanation
Indices: 1227978--1228030 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 19
1227968 AAAACCTCAT
1227978 TAAAATAATATTTAATATTC
1 TAAAAT-ATATTTAATATTC
*
1227998 TAAAATCAT-TATTAATATTT
1 TAAAAT-ATAT-TTAATATTC
1228018 TCAAAATATATTT
1 T-AAAATATATTT
1228031 CACTTTTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
19 1 0.04
20 21 0.75
21 6 0.21
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (19 bp):
TAAAATATATTTAATATTC
Found at i:1230874 original size:29 final size:30
Alignment explanation
Indices: 1230841--1230933 Score: 95
Period size: 29 Copynumber: 3.1 Consensus size: 30
1230831 ATTGGATGAA
1230841 TTTAGGGATGAAATTAG-AAGATTCAAAAG
1 TTTAGGGATGAAATTAGAAAGATTCAAAAG
* * *
1230870 TTTAGGGA-GTAATTTAGAAAGAGAGTCATAA-
1 TTTAGGGATG-AAATTAG-AA-AGATTCAAAAG
*
1230901 TTTAGGGATGAAATT-GAAATATTCAAAAG
1 TTTAGGGATGAAATTAGAAAGATTCAAAAG
1230930 TTTA
1 TTTA
1230934 AGAACTAATT
Statistics
Matches: 51, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
28 8 0.16
29 20 0.39
30 1 0.02
31 13 0.25
32 9 0.18
ACGTcount: A:0.43, C:0.03, G:0.23, T:0.31
Consensus pattern (30 bp):
TTTAGGGATGAAATTAGAAAGATTCAAAAG
Found at i:1239047 original size:23 final size:23
Alignment explanation
Indices: 1239021--1239076 Score: 103
Period size: 23 Copynumber: 2.4 Consensus size: 23
1239011 TCAATTTTGA
1239021 TTCGATTCAAGCATGAAATCAAC
1 TTCGATTCAAGCATGAAATCAAC
*
1239044 TTCGATTCAAGCATGAAATCTAC
1 TTCGATTCAAGCATGAAATCAAC
1239067 TTCGATTCAA
1 TTCGATTCAA
1239077 CCTTATAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.36, C:0.21, G:0.12, T:0.30
Consensus pattern (23 bp):
TTCGATTCAAGCATGAAATCAAC
Found at i:1242587 original size:5 final size:5
Alignment explanation
Indices: 1242581--1242624 Score: 70
Period size: 5 Copynumber: 8.8 Consensus size: 5
1242571 CGTCTCTTCT
* *
1242581 CGGCT CGGCT CGGCA CGGCA CGGCA CGGCA CGGCA CGGCA CGGC
1 CGGCA CGGCA CGGCA CGGCA CGGCA CGGCA CGGCA CGGCA CGGC
1242625 TCGTGGACGT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 38 1.00
ACGTcount: A:0.14, C:0.41, G:0.41, T:0.05
Consensus pattern (5 bp):
CGGCA
Found at i:1242948 original size:22 final size:22
Alignment explanation
Indices: 1242923--1242977 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
1242913 TCAGGATTTA
* *
1242923 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
1242945 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
1242967 CATGAGTTATA
1 CAGGAGTTATA
1242978 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.40
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:1248558 original size:15 final size:15
Alignment explanation
Indices: 1248519--1248565 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
1248509 CGTCTCGACA
*
1248519 CAGCACGGCTCGGCT
1 CAGCTCGGCTCGGCT
1248534 CAGCTCGGCTCGGCT
1 CAGCTCGGCTCGGCT
* * *
1248549 CGGCTTGGCTCAGCT
1 CAGCTCGGCTCGGCT
1248564 CA
1 CA
1248566 TTGTCGTGGT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.11, C:0.38, G:0.32, T:0.19
Consensus pattern (15 bp):
CAGCTCGGCTCGGCT
Found at i:1248565 original size:5 final size:5
Alignment explanation
Indices: 1248524--1248564 Score: 55
Period size: 5 Copynumber: 8.2 Consensus size: 5
1248514 CGACACAGCA
* * *
1248524 CGGCT CGGCT CAGCT CGGCT CGGCT CGGCT TGGCT CAGCT C
1 CGGCT CGGCT CGGCT CGGCT CGGCT CGGCT CGGCT CGGCT C
1248565 ATTGTCGTGG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.05, C:0.39, G:0.34, T:0.22
Consensus pattern (5 bp):
CGGCT
Found at i:1248881 original size:22 final size:22
Alignment explanation
Indices: 1248856--1248910 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
1248846 TCAGGAGTTA
* *
1248856 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * * *
1248878 CAGGGGTTACATGGTATAATTT
1 CAGGAGTTATATGATATAATTC
1248900 CAGGAGTTATA
1 CAGGAGTTATA
1248911 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:1254478 original size:5 final size:5
Alignment explanation
Indices: 1254456--1254495 Score: 53
Period size: 5 Copynumber: 8.0 Consensus size: 5
1254446 TCTCGTCTCA
* * *
1254456 GCTCG GCACG GCACG GCTCG GCTAG GCTCG GCTCG GCTCG
1 GCTCG GCTCG GCTCG GCTCG GCTCG GCTCG GCTCG GCTCG
1254496 TGGTTGTGGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.07, C:0.38, G:0.40, T:0.15
Consensus pattern (5 bp):
GCTCG
Found at i:1254817 original size:22 final size:22
Alignment explanation
Indices: 1254792--1254846 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
1254782 TCAGGAGTTA
* *
1254792 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
1254814 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
1254836 CAGGAGTTATA
1 CAGGAGTTATA
1254847 ATAGCTGAAT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.31, C:0.09, G:0.22, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:1258296 original size:22 final size:22
Alignment explanation
Indices: 1258271--1258313 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1258261 AACCCAAATT
*
1258271 AAATAATAATATGAAATAATAA
1 AAATAATAATAAGAAATAATAA
* *
1258293 AAATTATAATAAGTAATAATA
1 AAATAATAATAAGAAATAATA
1258314 TATAATATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (22 bp):
AAATAATAATAAGAAATAATAA
Found at i:1259554 original size:20 final size:19
Alignment explanation
Indices: 1259531--1259610 Score: 79
Period size: 20 Copynumber: 3.9 Consensus size: 19
1259521 CATGTTTTTA
*
1259531 TTTTTTATTTTATTTTTCAT
1 TTTTTTATTTTATTATT-AT
1259551 TTTTTACTATTTTTATTATTAT
1 TTTTT--TA-TTTTATTATTAT
*
1259573 TTTGTTTCTTTTATTATTAT
1 TTT-TTTATTTTATTATTAT
*
1259593 TTTTATATTATTATTATT
1 TTTTTTATT-TTATTATT
1259611 TTCAGTGTTT
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
19 4 0.08
20 28 0.55
21 1 0.02
22 7 0.14
23 11 0.22
ACGTcount: A:0.20, C:0.04, G:0.01, T:0.75
Consensus pattern (19 bp):
TTTTTTATTTTATTATTAT
Found at i:1259584 original size:29 final size:28
Alignment explanation
Indices: 1259544--1259612 Score: 59
Period size: 31 Copynumber: 2.4 Consensus size: 28
1259534 TTTATTTTAT
*
1259544 TTTTCATTTTTTACTATTTTTATTATTA
1 TTTTTATTTTTTACTATTTTTATTATTA
* *
1259572 TTTTGT-TTCTTTTATTATTATTTTTATATTA
1 TTTT-TATT-TTTTACTATT-TTTAT-TATTA
*
1259603 TTATTATTTT
1 TTTTTATTTT
1259613 CAGTGTTTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
28 6 0.19
29 9 0.28
30 7 0.22
31 10 0.31
ACGTcount: A:0.20, C:0.04, G:0.01, T:0.74
Consensus pattern (28 bp):
TTTTTATTTTTTACTATTTTTATTATTA
Found at i:1259623 original size:20 final size:17
Alignment explanation
Indices: 1259533--1259612 Score: 80
Period size: 17 Copynumber: 4.9 Consensus size: 17
1259523 TGTTTTTATT
1259533 TTTTATT-TTATTTTTCA
1 TTTTATTATTATTTTT-A
*
1259550 TTTT-TTACTATTTTTA
1 TTTTATTATTATTTTTA
*
1259566 --TTATTATT-TTGTTTC
1 TTTTATTATTATT-TTTA
1259581 TTTTATTATTATTTTTA
1 TTTTATTATTATTTTTA
*
1259598 TATTATTATTATTTT
1 TTTTATTATTATTTT
1259613 CAGTGTTTTA
Statistics
Matches: 52, Mismatches: 5, Indels: 12
0.75 0.07 0.17
Matches are distributed among these distances:
14 4 0.08
15 7 0.13
16 3 0.06
17 36 0.69
18 2 0.04
ACGTcount: A:0.20, C:0.04, G:0.01, T:0.75
Consensus pattern (17 bp):
TTTTATTATTATTTTTA
Found at i:1259700 original size:2 final size:2
Alignment explanation
Indices: 1259691--1259774 Score: 72
Period size: 2 Copynumber: 45.0 Consensus size: 2
1259681 TAAATACTAC
* * * *
1259691 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT TT TT TT AT TT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
1259731 AT TT AT -T AT A- AC AT -T A- 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
1259769 AT AT AT
1 AT AT AT
1259775 TTACTTTATT
Statistics
Matches: 69, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
1 6 0.09
2 63 0.91
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (2 bp):
AT
Found at i:1260193 original size:21 final size:20
Alignment explanation
Indices: 1260154--1260231 Score: 72
Period size: 21 Copynumber: 4.0 Consensus size: 20
1260144 ATTTTTTCTT
* *
1260154 TGTTTTATTTTATTT-TTTA
1 TGTTATATTTTTTTTATTTA
*
1260173 TATTATATTTTTTTGTATTTA
1 TGTTATATTTTTTT-TATTTA
*
1260194 TGTTATCATTTTATTTATTT-
1 TGTTAT-ATTTTTTTTATTTA
*
1260214 TGTT-TATTTTTTTCATTT
1 TGTTATATTTTTTTTATTT
1260232 TTTCTTCGTT
Statistics
Matches: 49, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
18 11 0.22
19 12 0.24
20 5 0.10
21 14 0.29
22 7 0.14
ACGTcount: A:0.18, C:0.03, G:0.05, T:0.74
Consensus pattern (20 bp):
TGTTATATTTTTTTTATTTA
Found at i:1260234 original size:29 final size:29
Alignment explanation
Indices: 1260202--1260257 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
1260192 TATGTTATCA
* *
1260202 TTTTATTTATTTTGTTTATTTTTTTCATT
1 TTTTATTCATTTTGTTTATTATTTTCATT
* *
1260231 TTTTCTTCGTTTTGTTTATTATTTTCA
1 TTTTATTCATTTTGTTTATTATTTTCA
1260258 CATTTACACA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.12, C:0.07, G:0.05, T:0.75
Consensus pattern (29 bp):
TTTTATTCATTTTGTTTATTATTTTCATT
Found at i:1262954 original size:95 final size:95
Alignment explanation
Indices: 1262840--1263080 Score: 297
Period size: 95 Copynumber: 2.5 Consensus size: 95
1262830 ATAATATATA
* * * * *
1262840 TATATATATACAATAAAGCTTGAGCTGTCTCTCTAAAGCAATTGGTTAAACACCTCGGCTTTTTG
1 TATA-ATATACAATAAAGCTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACACATCGGCTTTATA
* *
1262905 GATAAGGTTCAACTAGCCTAATAAAGATGAT
65 GATAAGATTCAACTAGCATAATAAAGATGAT
* *
1262936 TATAATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCATCGGCTTTATAG
1 TATAATATACAATAAAGCTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACACATCGGCTTTATAG
* * * *
1263001 ATAATATTCAGCTAGCATGATAAGGATGAT
66 ATAAGATTCAACTAGCATAATAAAGATGAT
* *
1263031 TATAATATCTACAATGATA--TTGAGCTGTCCCTCTAGAGCGATTGGTTAAA
1 TATAATA--TACAAT-AAAGCTTGAGCTGTCCCTCTAGAGCAATTGGTTAAA
1263081 TGCCCCAGCT
Statistics
Matches: 126, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
95 85 0.67
96 33 0.26
97 6 0.05
98 2 0.02
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (95 bp):
TATAATATACAATAAAGCTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACACATCGGCTTTATAG
ATAAGATTCAACTAGCATAATAAAGATGAT
Found at i:1264360 original size:83 final size:83
Alignment explanation
Indices: 1264221--1265274 Score: 1230
Period size: 84 Copynumber: 12.7 Consensus size: 83
1264211 CTATTGGCAT
* * * *
1264221 CATAACTCAAAGCGAGAAGGGTTATCTGTCAGCCAAGACCTTCGAGTTCGATTACACTCAGCTCA
1 CATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCA
* *
1264286 AAGACACATCATTTACAA
66 AAGGCACATCATTTACAG
* * * * *
1264304 CATAACTCAAGACGATAAGGGTTATCTGTCAACAAAGACCTTCAAGTTCAATTACACTCAGCTCA
1 CATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCA
*
1264369 AAGGCACATCGTTTACAG
66 AAGGCACATCATTTACAG
* * * *
1264387 CATAACTCAAGGCTAGAAGGGTTATCTGTCAACAAAGACCTTTGAGTTCAATTACACTCAGCTCA
1 CATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCA
* **
1264452 AAGGCATATCATTTGTAG
66 AAGGCACATCATTTACAG
* * * * * * * *
1264470 TATAACTCAAGGCTAGAAAGGCTATCT-TCCAATAAAATACCTTCGAGCTCGATTACACTCAGCT
1 CATAGCTCAAGGCGAGAAGGGTTATCTGT-CAA-CAAAGACCTTCGAGTTCGATTACACTCAGCT
1264534 CAAAGGCACATCATTTACAG
64 CAAAGGCACATCATTTACAG
* * * * * * *
1264554 CATTGCTCAAGGCAAGAAGGGCTATATG-C--CAAAAACCTTCGAGTTTGATTACACTTAGCTCA
1 CATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCA
1264616 AAGGCACATCATTTGA-AG
66 AAGGCACATCATTT-ACAG
* * * *
1264634 CATAGCTTAAGGCAAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGATT-GATTACACTCAGCT
1 CATAGCTCAAGGCGAGAAGGGTTATCTGTCAAC-AAAGACCTTCGAG-TTCGATTACACTCAGCT
**
1264698 CAAAGGCACATCATTTGTAG
64 CAAAGGCACATCATTTACAG
* * *
1264718 CATAGTTCAAGGCAAGAAGGGTTATC--T-ACCAAAGACCTTCGAGTTCGATTACACTCAGCTCA
1 CATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCA
1264780 AAGGCACATCATTTACAG
66 AAGGCACATCATTTACAG
* * * * *
1264798 TATAACTCAAGGCTAGAAGAGTTA-CT-TCAACAAAGACCTTTGAGTTCGATTACACTCAGCTCA
1 CATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCA
*
1264861 AAGGCACATCATTTACAA
66 AAGGCACATCATTTACAG
* * * * *
1264879 CATAGCTCAAGGCGAGAAGGGTTATCTGCCAACAAAAGACCTTCGAATTCGATTATACTCAACTG
1 CATAGCTCAAGGCGAGAAGGGTTATCTGTCAAC-AAAGACCTTCGAGTTCGATTACACTCAGCTC
* *
1264944 AAAGGCTCATCATTTGCAG
65 AAAGGCACATCATTTACAG
* * * *
1264963 CATAGCTCAAGGCGAGAATGGTTATCTGCCAACAAAAGACCTTCGAGTTTGATTACTCTCAGCTC
1 CATAGCTCAAGGCGAGAAGGGTTATCTGTCAAC-AAAGACCTTCGAGTTCGATTACACTCAGCTC
*
1265028 AAAGGCACATCATTTGCAG
65 AAAGGCACATCATTTACAG
* * * * *
1265047 CATAGCTCAAGGCAAGAAAGGCTATCTGCCAACAAAAGACATTCGAGTTCGATTACACTCAGCTC
1 CATAGCTCAAGGCGAGAAGGGTTATCTGTCAAC-AAAGACCTTCGAGTTCGATTACACTCAGCTC
*
1265112 AAAGGCATATCAAATTTACAG
65 AAAGGCACATC--ATTTACAG
* **
1265133 CATAGCTCAAGGCGAGAAGGGCTATCTACCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTC
1 CATAGCTCAAGGCGAGAAGGGTTATCTGTCAAC-AAAGACCTTCGAGTTCGATTACACTCAGCTC
*
1265198 AAAGGCATATCAAATTTACAG
65 AAAGGCACATC--ATTTACAG
* * * * *
1265219 CATAGATCAAGGCGAGAAGGGCTATCTGTTAATAAATACCTTCGAGTTCGATTACA
1 CATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACA
1265275 TTCACAAAGG
Statistics
Matches: 852, Mismatches: 101, Indels: 34
0.86 0.10 0.03
Matches are distributed among these distances:
79 3 0.00
80 134 0.16
81 74 0.09
82 3 0.00
83 180 0.21
84 317 0.37
85 24 0.03
86 117 0.14
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (83 bp):
CATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCAGCTCA
AAGGCACATCATTTACAG
Found at i:1264690 original size:164 final size:166
Alignment explanation
Indices: 1264221--1265274 Score: 1212
Period size: 164 Copynumber: 6.3 Consensus size: 166
1264211 CTATTGGCAT
* * * * * * *
1264221 CATAACTCAAAGCGAGAAGGGTTATCTGTCAGCCAAGACCTTCGAGTTCGATTACACTCAGCTCA
1 CATAGCTCAAGGCAAGAAGGGCTATCTGCCA-CAAAAACCTTCGAGTTCGATTACACTCAGCTCA
* * * * * * *
1264286 AAGACACATCATTTACAACATAACTCAAGACGATAAGGGTTATCTGTCAAC-AAAGACCTTCAAG
65 AAGGCACATCATTTACAGCATAACTCAAGGCGAGAAGGGCTATCTGCCAACAAAAGACCTTCGAG
* *
1264350 TTCAATTACACTCAGCTCAAAGGCACATCGTTTACAG
130 TTCGATTACACTCAGCTCAAAGGCACATCATTTACAG
* * * * * * *
1264387 CATAACTCAAGGCTAGAAGGGTTATCTGTCAACAAAGACCTTTGAGTTCAATTACACTCAGCTCA
1 CATAGCTCAAGGCAAGAAGGGCTATCTG-CCACAAAAACCTTCGAGTTCGATTACACTCAGCTCA
* ** * * * * * *
1264452 AAGGCATATCATTTGTAGTATAACTCAAGGCTAGAAAGGCTATCTTCCAATAAAATACCTTCGAG
65 AAGGCACATCATTTACAGCATAACTCAAGGCGAGAAGGGCTATCTGCCAACAAAAGACCTTCGAG
*
1264517 CTCGATTACACTCAGCTCAAAGGCACATCATTTACAG
130 TTCGATTACACTCAGCTCAAAGGCACATCATTTACAG
* * * *
1264554 CATTGCTCAAGGCAAGAAGGGCTATATG-C-CAAAAACCTTCGAGTTTGATTACACTTAGCTCAA
1 CATAGCTCAAGGCAAGAAGGGCTATCTGCCACAAAAACCTTCGAGTTCGATTACACTCAGCTCAA
* * *
1264617 AGGCACATCATTTGA-AGCATAGCTTAAGGCAAGAAGGGCTATCTGCCAACAAAAGACCTTCGAG
66 AGGCACATCATTT-ACAGCATAACTCAAGGCGAGAAGGGCTATCTGCCAACAAAAGACCTTCGAG
**
1264681 ATT-GATTACACTCAGCTCAAAGGCACATCATTTGTAG
130 -TTCGATTACACTCAGCTCAAAGGCACATCATTTACAG
* * * *
1264718 CATAGTTCAAGGCAAGAAGGGTTATCT-AC-CAAAGACCTTCGAGTTCGATTACACTCAGCTCAA
1 CATAGCTCAAGGCAAGAAGGGCTATCTGCCACAAAAACCTTCGAGTTCGATTACACTCAGCTCAA
* * * * * *
1264781 AGGCACATCATTTACAGTATAACTCAAGGCTAGAAGAGTTA-CT-TCAAC-AAAGACCTTTGAGT
66 AGGCACATCATTTACAGCATAACTCAAGGCGAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGT
*
1264843 TCGATTACACTCAGCTCAAAGGCACATCATTTACAA
131 TCGATTACACTCAGCTCAAAGGCACATCATTTACAG
* * * * * *
1264879 CATAGCTCAAGGCGAGAAGGGTTATCTGCCAACAAAAGACCTTCGAATTCGATTATACTCAACTG
1 CATAGCTCAAGGCAAGAAGGGCTATCTGCC-ACAAAA-ACCTTCGAGTTCGATTACACTCAGCTC
* * * * *
1264944 AAAGGCTCATCATTTGCAGCATAGCTCAAGGCGAGAATGGTTATCTGCCAACAAAAGACCTTCGA
64 AAAGGCACATCATTTACAGCATAACTCAAGGCGAGAAGGGCTATCTGCCAACAAAAGACCTTCGA
* * *
1265009 GTTTGATTACTCTCAGCTCAAAGGCACATCATTTGCAG
129 GTTCGATTACACTCAGCTCAAAGGCACATCATTTACAG
* *
1265047 CATAGCTCAAGGCAAGAAAGGCTATCTGCCAACAAAAGACATTCGAGTTCGATTACACTCAGCTC
1 CATAGCTCAAGGCAAGAAGGGCTATCTGCC-ACAAAA-ACCTTCGAGTTCGATTACACTCAGCTC
* * *
1265112 AAAGGCATATCAAATTTACAGCATAGCTCAAGGCGAGAAGGGCTATCTACCAACAAAAGACCTTC
64 AAAGGCACATC--ATTTACAGCATAACTCAAGGCGAGAAGGGCTATCTGCCAACAAAAGACCTTC
*
1265177 GAGTTCGATTACACTCAGCTCAAAGGCATATCAAATTTACAG
127 GAGTTCGATTACACTCAGCTCAAAGGCACATC--ATTTACAG
* * **
1265219 CATAGATCAAGGCGAGAAGGGCTATCTGTTA-ATAAATACCTTCGAGTTCGATTACA
1 CATAGCTCAAGGCAAGAAGGGCTATCTGCCACA-AAA-ACCTTCGAGTTCGATTACA
1265275 TTCACAAAGG
Statistics
Matches: 755, Mismatches: 114, Indels: 33
0.84 0.13 0.04
Matches are distributed among these distances:
160 2 0.00
161 68 0.09
162 5 0.01
163 3 0.00
164 206 0.27
165 60 0.08
166 95 0.13
167 73 0.10
168 111 0.15
170 78 0.10
171 22 0.03
172 32 0.04
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (166 bp):
CATAGCTCAAGGCAAGAAGGGCTATCTGCCACAAAAACCTTCGAGTTCGATTACACTCAGCTCAA
AGGCACATCATTTACAGCATAACTCAAGGCGAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGT
TCGATTACACTCAGCTCAAAGGCACATCATTTACAG
Found at i:1265326 original size:82 final size:83
Alignment explanation
Indices: 1265047--1265357 Score: 225
Period size: 86 Copynumber: 3.7 Consensus size: 83
1265037 TCATTTGCAG
* * * * * ** * *
1265047 CATAGCTCAAGGCAAGAAAGGCTATCTGCCAACAAAAGACATTCGAGTTCGATTACACTCAGCTC
1 CATAGATCAAGGCGAGAAAGACTATCAGTCAATGAAA-ACCTTCGAGTTCGATTACATTCA-C-C
* *
1265112 AAAGGCATATCAAATTTACAG
63 AAAGGCATATCAAATTCACAA
* * * * ** *
1265133 CATAGCTCAAGGCGAGAAGGGCTATCTA-CCAACAAAAGACCTTCGAGTTCGATTACACTCAGCT
1 CATAGATCAAGGCGAGAAAGACTATC-AGTCAATGAAA-ACCTTCGAGTTCGATTACATTCA-C-
* *
1265197 CAAAGGCATATCAAATTTACAG
62 CAAAGGCATATCAAATTCACAA
* * * *
1265219 CATAGATCAAGGCGAGAAGGGCTATCTGTTAAT-AAATACCTTCGAGTTCGATTACATTCA-CAA
1 CATAGATCAAGGCGAGAAAGACTATCAGTCAATGAAA-ACCTTCGAGTTCGATTACATTCACCAA
*
1265282 AGGCATGTCAAATTCACAA
65 AGGCATATCAAATTCACAA
* * ** * * * *
1265301 TATAGCTTTAGTCGAGAAATACTATCAGTCAATGAAAA-CTTTGAGTTCGATTCCATT
1 CATAGATCAAGGCGAGAAAGACTATCAGTCAATGAAAACCTTCGAGTTCGATTACATT
1265358 TAGCTCGATG
Statistics
Matches: 196, Mismatches: 26, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
81 17 0.09
82 43 0.22
83 3 0.02
85 25 0.13
86 108 0.55
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.25
Consensus pattern (83 bp):
CATAGATCAAGGCGAGAAAGACTATCAGTCAATGAAAACCTTCGAGTTCGATTACATTCACCAAA
GGCATATCAAATTCACAA
Found at i:1267087 original size:3 final size:3
Alignment explanation
Indices: 1267076--1267190 Score: 82
Period size: 3 Copynumber: 39.3 Consensus size: 3
1267066 ATTTTTTTAC
* * *
1267076 TAT TTT TAT TAT T-T TTT TCT T-T TAT TAT TAT T-T T-T TA- TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
1267119 TAT TAT TTT TAG TGT T-T TAT ACAT GTA- TAT ATAT ATAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT -TAT -TAT TAT -TAT -TAT TAT TAT TAT
1267166 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
1267191 TTCCTCATAT
Statistics
Matches: 93, Mismatches: 11, Indels: 16
0.77 0.09 0.13
Matches are distributed among these distances:
2 14 0.15
3 69 0.74
4 10 0.11
ACGTcount: A:0.28, C:0.02, G:0.03, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1267091 original size:9 final size:9
Alignment explanation
Indices: 1267049--1267192 Score: 80
Period size: 9 Copynumber: 15.8 Consensus size: 9
1267039 TATCATGTTT
*
1267049 TTATTTTCA
1 TTATTTTTA
*
1267058 TTATTTTCA
1 TTATTTTTA
1267067 TT-TTTTTA
1 TTATTTTTA
*
1267075 CTATTTTTA
1 TTATTTTTA
1267084 TTATTTTT-
1 TTATTTTTA
*
1267092 TTCTTTTATTA
1 TT-ATTT-TTA
1267103 TTATTTTT-
1 TTATTTTTA
*
1267111 TATATTATTA
1 T-TATTTTTA
1267121 TTATTTTTA
1 TTATTTTTA
* *
1267130 GT-GTTTTA
1 TTATTTTTA
* * *
1267138 TACATGTATA
1 T-TATTTTTA
*
1267148 TATATATATTA
1 T-TAT-TTTTA
*
1267159 TTATTATTA
1 TTATTTTTA
*
1267168 TTATTATTA
1 TTATTTTTA
*
1267177 TTATTATTA
1 TTATTTTTA
1267186 TTATTTT
1 TTATTTT
1267193 CCTCATATTT
Statistics
Matches: 107, Mismatches: 19, Indels: 18
0.74 0.13 0.12
Matches are distributed among these distances:
8 14 0.13
9 72 0.67
10 16 0.15
11 5 0.05
ACGTcount: A:0.26, C:0.03, G:0.02, T:0.69
Consensus pattern (9 bp):
TTATTTTTA
Found at i:1267273 original size:2 final size:2
Alignment explanation
Indices: 1267266--1267300 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1267256 ATTCTAACGT
1267266 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 T
1267301 TTACTTTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1267584 original size:14 final size:14
Alignment explanation
Indices: 1267565--1267611 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
1267555 TAATTCCATT
1267565 TTTTCTTTGTTTTA
1 TTTTCTTTGTTTTA
1267579 TTTTCTTT-TTTTA
1 TTTTCTTTGTTTTA
* * *
1267592 TATTATTTGTTTTG
1 TTTTCTTTGTTTTA
1267606 TTTTCT
1 TTTTCT
1267612 ATATTTGTGT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
13 11 0.41
14 16 0.59
ACGTcount: A:0.09, C:0.06, G:0.06, T:0.79
Consensus pattern (14 bp):
TTTTCTTTGTTTTA
Found at i:1268155 original size:10 final size:10
Alignment explanation
Indices: 1268113--1268178 Score: 52
Period size: 10 Copynumber: 6.8 Consensus size: 10
1268103 ACTATGTAAA
1268113 ATATAATA-T
1 ATATAATATT
*
1268122 ATATACTATAT
1 ATATAATAT-T
1268133 ACTATAAATATT
1 A-TAT-AATATT
*
1268145 ATATGATATT
1 ATATAATATT
1268155 ATAT-A-A-T
1 ATATAATATT
1268162 ATA-AATATT
1 ATATAATATT
1268171 ATATAATA
1 ATATAATA
1268179 AAGTAATAGT
Statistics
Matches: 46, Mismatches: 3, Indels: 15
0.72 0.05 0.23
Matches are distributed among these distances:
7 5 0.11
8 2 0.04
9 12 0.26
10 13 0.28
11 5 0.11
12 5 0.11
13 4 0.09
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.44
Consensus pattern (10 bp):
ATATAATATT
Found at i:1268164 original size:26 final size:25
Alignment explanation
Indices: 1268119--1268175 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 25
1268109 TAAAATATAA
*
1268119 TATATATACTATATACTATAAATAT
1 TATATATACTATATAATATAAATAT
*
1268144 TATATGATATTATATAATATAAATAT
1 TATAT-ATACTATATAATATAAATAT
1268170 TATATA
1 TATATA
1268176 ATAAAGTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 6 0.21
26 23 0.79
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.46
Consensus pattern (25 bp):
TATATATACTATATAATATAAATAT
Found at i:1268176 original size:16 final size:16
Alignment explanation
Indices: 1268062--1268178 Score: 87
Period size: 16 Copynumber: 7.1 Consensus size: 16
1268052 CGACAATACC
1268062 ATATAATATATATACCAT
1 ATATAATATATATA--AT
1268080 ATTATAA-ACTATATAAT
1 A-TATAATA-TATATAAT
* *
1268097 ATA-AATACTATGTAAA
1 ATATAATA-TATATAAT
*
1268113 ATATAATATATATACT
1 ATATAATATATATAAT
* * *
1268129 ATATACTATAAATATT
1 ATATAATATATATAAT
*
1268145 ATATGATATTATATAAT
1 ATATAATA-TATATAAT
1268162 ATA-AATATTATATAAT
1 ATATAATA-TATATAAT
1268178 A
1 A
1268179 AAGTAATAGT
Statistics
Matches: 81, Mismatches: 13, Indels: 12
0.76 0.12 0.11
Matches are distributed among these distances:
15 2 0.02
16 50 0.62
17 16 0.20
18 2 0.02
19 11 0.14
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (16 bp):
ATATAATATATATAAT
Found at i:1271249 original size:19 final size:19
Alignment explanation
Indices: 1271205--1271249 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
1271195 TAGCAAGGGT
*
1271205 GAAAAAGAAAATAATGAAA
1 GAAAAATAAAATAATGAAA
1271224 GAAAAATAAAA-AGATGAAA
1 GAAAAATAAAATA-ATGAAA
1271243 GAAAAAT
1 GAAAAAT
1271250 TGAACTTCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 1 0.04
19 23 0.96
ACGTcount: A:0.73, C:0.00, G:0.16, T:0.11
Consensus pattern (19 bp):
GAAAAATAAAATAATGAAA
Found at i:1271471 original size:41 final size:38
Alignment explanation
Indices: 1271402--1271488 Score: 129
Period size: 41 Copynumber: 2.2 Consensus size: 38
1271392 AATAACTAAT
*
1271402 TCCTAAATAAAATAATAATAAAATAATCAAACTAAAAA
1 TCCTAAATAAAATAATAATAAAACAATCAAACTAAAAA
1271440 TCCTAAATAAAAAATTAATAATAAAACAATCAAACTAAAAA
1 TCCTAAAT--AAAA-TAATAATAAAACAATCAAACTAAAAA
*
1271481 TCATAAAT
1 TCCTAAAT
1271489 CTAAAAGGTT
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
38 8 0.18
40 4 0.09
41 32 0.73
ACGTcount: A:0.64, C:0.11, G:0.00, T:0.24
Consensus pattern (38 bp):
TCCTAAATAAAATAATAATAAAACAATCAAACTAAAAA
Found at i:1284383 original size:7 final size:7
Alignment explanation
Indices: 1284371--1284425 Score: 53
Period size: 7 Copynumber: 8.3 Consensus size: 7
1284361 ATAATTTCTT
1284371 AAAGAAA
1 AAAGAAA
1284378 AAAGAAA
1 AAAGAAA
*
1284385 AAATAAA
1 AAAGAAA
1284392 AAA-AAA
1 AAAGAAA
1284398 AAA-AAA
1 AAAGAAA
**
1284404 AAA-CTA
1 AAAGAAA
1284410 AAAGAAA
1 AAAGAAA
*
1284417 AATGAAA
1 AAAGAAA
1284424 AA
1 AA
1284426 TAAATAAAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
6 16 0.39
7 25 0.61
ACGTcount: A:0.85, C:0.02, G:0.07, T:0.05
Consensus pattern (7 bp):
AAAGAAA
Found at i:1284424 original size:20 final size:19
Alignment explanation
Indices: 1284371--1284429 Score: 75
Period size: 19 Copynumber: 3.1 Consensus size: 19
1284361 ATAATTTCTT
1284371 AAAGAAAAAAGAAAAAATA
1 AAAGAAAAAAGAAAAAATA
* *
1284390 AAAAAAAAAAAAAAAAACTA
1 AAAGAAAAAAGAAAAAA-TA
*
1284410 AAAGAAAAATG-AAAAATA
1 AAAGAAAAAAGAAAAAATA
1284428 AA
1 AA
1284430 TAAAATGAGG
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
18 4 0.12
19 20 0.59
20 10 0.29
ACGTcount: A:0.85, C:0.02, G:0.07, T:0.07
Consensus pattern (19 bp):
AAAGAAAAAAGAAAAAATA
Found at i:1293455 original size:30 final size:30
Alignment explanation
Indices: 1293421--1293478 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
1293411 TTTATTAATT
1293421 ATATTGAAATTCAAGGGTAAATTGGTAAAA
1 ATATTGAAATTCAAGGGTAAATTGGTAAAA
* * *
1293451 ATATTTAATTTTAAGGGTAAATTGGTAA
1 ATATTGAAATTCAAGGGTAAATTGGTAA
1293479 TTTTGCATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.43, C:0.02, G:0.19, T:0.36
Consensus pattern (30 bp):
ATATTGAAATTCAAGGGTAAATTGGTAAAA
Found at i:1302607 original size:103 final size:103
Alignment explanation
Indices: 1302419--1303111 Score: 825
Period size: 103 Copynumber: 6.9 Consensus size: 103
1302409 AGAAACAATG
* * * * * *
1302419 TGAGATAAAATTTTGTTTCGAGAGAAACAATTTCAAAATTTATGTTTTAAGGGAAAACTATCA-C
1 TGAGATAAATTTTTGTTTCGAGTGAAAGAATTTCAAAATTTGTGTTTCAAGGGAAAACT-GCATC
* * *
1302483 AAGAGAGACGAAATTGATTTTAAGAAAAACTATCTCAAA
65 AAGCGAGACGAAACTGATTTTAAGAAAAACCATCTCAAA
* * * * *
1302522 TGAAATAAAGTTTTGTTTCAATTGAAA-ATTTTTCAAAATTTGTGTTTCAAGGGAAAACTGCATC
1 TGAGATAAATTTTTGTTTCGAGTGAAAGA-ATTTCAAAATTTGTGTTTCAAGGGAAAACTGCATC
*
1302586 AAGCGAGACGAAACTGGTTTTAAGAAAAACCATCTCAAA
65 AAGCGAGACGAAACTGATTTTAAGAAAAACCATCTCAAA
*
1302625 TGAGATAAATTTTTGTTTCGAGTGAAAGAATTTCAAAATTTGTGTTTAAAGGGAAAACTGTC-TC
1 TGAGATAAATTTTTGTTTCGAGTGAAAGAATTTCAAAATTTGTGTTTCAAGGGAAAACTG-CATC
* * * * * *
1302689 GAGCGAGATGAAATTGATTTTAATAAAAACTATCTCAAG
65 AAGCGAGACGAAACTGATTTTAAGAAAAACCATCTCAAA
*
1302728 TGAGATAAA-TTTTGTTTCGAGTG-AAGCAATTTCAAAATTTGTCTTTCAAGGGAAAACTGCATC
1 TGAGATAAATTTTTGTTTCGAGTGAAAG-AATTTCAAAATTTGTGTTTCAAGGGAAAACTGCATC
* *
1302791 AAGCGAGATGAAACTTATTTTAAGAAAAACCATCTCAAA
65 AAGCGAGACGAAACTGATTTTAAGAAAAACCATCTCAAA
1302830 TGAGATAAATTTTTGTTTCGAGTGAAAGAATTTCAAAATTTGTGTTTCAAGGGAAAACTGCAT--
1 TGAGATAAATTTTTGTTTCGAGTGAAAGAATTTCAAAATTTGTGTTTCAAGGGAAAACTGCATCA
1302893 -------C--AA-TGATTTTAAGAAAAACCATCTCAAA
66 AGCGAGACGAAACTGATTTTAAGAAAAACCATCTCAAA
* * *
1302921 TGAGATAAATTTTTGTTTCGAGTGAAATAATTTCAAAATTTCTGTTTCAAGGGAAAACTATC-TC
1 TGAGATAAATTTTTGTTTCGAGTGAAAGAATTTCAAAATTTGTGTTTCAAGGGAAAACT-GCATC
* * * * *
1302985 AAGTGAGATGAAACTGATTTAAAGAAAAACCATCCCAAG
65 AAGCGAGACGAAACTGATTTTAAGAAAAACCATCTCAAA
* * * * *
1303024 TGAGATAAATTTTTGTTT-AAGTGAAACAATTTTAGAATTT-TGTTTCAAGGGAAAACTATC-TC
1 TGAGATAAATTTTTGTTTCGAGTGAAAGAATTTCAAAATTTGTGTTTCAAGGGAAAACT-GCATC
* *
1303086 AAGCGAGACGAAATTGATATTAAGAA
65 AAGCGAGACGAAACTGATTTTAAGAA
1303112 CATCTACATC
Statistics
Matches: 516, Mismatches: 53, Indels: 44
0.84 0.09 0.07
Matches are distributed among these distances:
91 82 0.16
92 3 0.01
101 47 0.09
102 111 0.22
103 268 0.52
104 5 0.01
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.32
Consensus pattern (103 bp):
TGAGATAAATTTTTGTTTCGAGTGAAAGAATTTCAAAATTTGTGTTTCAAGGGAAAACTGCATCA
AGCGAGACGAAACTGATTTTAAGAAAAACCATCTCAAA
Found at i:1302814 original size:205 final size:204
Alignment explanation
Indices: 1302419--1303111 Score: 905
Period size: 205 Copynumber: 3.4 Consensus size: 204
1302409 AGAAACAATG
* * * * *
1302419 TGAGATAAAATTTTGTTTCGAGAGAAACAATTTCAAAATTTATGTTTTAAGGGAAAACTATCACA
1 TGAGATAAATTTTTGTTTCGAGTGAAACAATTTCAAAATTTGTGTTTCAAGGGAAAACTATCTCA
* * * *
1302484 AGAGAGACGAAATTGATTTTAAGAAAAACTATCTCAAATGAAATAAAGTTTTGTTTCAATTGAAA
66 AGCGAGACGAAATTGATTTTAAGAAAAACTATCTCAAATGAGATAAAGTTTTGTTTCGAGTGAAA
* *
1302549 ATTTTTCAAAATTTGTGTTTCAAGGGAAAACTGCATCAAGCGAGACGAAACTGGTTTTAAGAAAA
131 A--TTTCAAAATTTGTGTTTCAAGGGAAAACTGCATCAAGCGAGATGAAACTGATTTTAAGAAAA
1302614 ACCATCTCAAA
194 ACCATCTCAAA
* * * *
1302625 TGAGATAAATTTTTGTTTCGAGTGAAAGAATTTCAAAATTTGTGTTTAAAGGGAAAACTGTCTCG
1 TGAGATAAATTTTTGTTTCGAGTGAAACAATTTCAAAATTTGTGTTTCAAGGGAAAACTATCTCA
* * *
1302690 AGCGAGATGAAATTGATTTTAATAAAAACTATCTCAAGTGAGATAAA-TTTTGTTTCGAGTGAAG
66 AGCGAGACGAAATTGATTTTAAGAAAAACTATCTCAAATGAGATAAAGTTTTGTTTCGAGTGAA-
* *
1302754 CAATTTCAAAATTTGTCTTTCAAGGGAAAACTGCATCAAGCGAGATGAAACTTATTTTAAGAAAA
130 -AATTTCAAAATTTGTGTTTCAAGGGAAAACTGCATCAAGCGAGATGAAACTGATTTTAAGAAAA
1302819 ACCATCTCAAA
194 ACCATCTCAAA
*
1302830 TGAGATAAATTTTTGTTTCGAGTGAAAGAATTTCAAAATTTGTGTTTCAAGGG-AAA--A-CT--
1 TGAGATAAATTTTTGTTTCGAGTGAAACAATTTCAAAATTTGTGTTTCAAGGGAAAACTATCTCA
* * *
1302889 -GC-A-TC--AA-TGATTTTAAGAAAAACCATCTCAAATGAGATAAATTTTTGTTTCGAGTGAAA
66 AGCGAGACGAAATTGATTTTAAGAAAAACTATCTCAAATGAGATAAAGTTTTGTTTCGAGTG-AA
* * * *
1302948 TAATTTCAAAATTTCTGTTTCAAGGGAAAACTATC-TCAAGTGAGATGAAACTGATTTAAAGAAA
130 -AATTTCAAAATTTGTGTTTCAAGGGAAAACT-GCATCAAGCGAGATGAAACTGATTTTAAGAAA
* *
1303012 AACCATCCCAAG
193 AACCATCTCAAA
* * *
1303024 TGAGATAAATTTTTGTTT-AAGTGAAACAATTTTAGAATTT-TGTTTCAAGGGAAAACTATCTCA
1 TGAGATAAATTTTTGTTTCGAGTGAAACAATTTCAAAATTTGTGTTTCAAGGGAAAACTATCTCA
*
1303087 AGCGAGACGAAATTGATATTAAGAA
66 AGCGAGACGAAATTGATTTTAAGAA
1303112 CATCTACATC
Statistics
Matches: 429, Mismatches: 41, Indels: 36
0.85 0.08 0.07
Matches are distributed among these distances:
192 11 0.03
193 52 0.12
194 99 0.23
195 4 0.01
196 2 0.00
197 1 0.00
198 2 0.00
199 2 0.00
200 1 0.00
201 3 0.01
203 2 0.00
204 14 0.03
205 135 0.31
206 99 0.23
207 2 0.00
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.32
Consensus pattern (204 bp):
TGAGATAAATTTTTGTTTCGAGTGAAACAATTTCAAAATTTGTGTTTCAAGGGAAAACTATCTCA
AGCGAGACGAAATTGATTTTAAGAAAAACTATCTCAAATGAGATAAAGTTTTGTTTCGAGTGAAA
ATTTCAAAATTTGTGTTTCAAGGGAAAACTGCATCAAGCGAGATGAAACTGATTTTAAGAAAAAC
CATCTCAAA
Found at i:1303031 original size:194 final size:191
Alignment explanation
Indices: 1302703--1303080 Score: 560
Period size: 194 Copynumber: 2.0 Consensus size: 191
1302693 GAGATGAAAT
* * * *
1302703 TGATTTTAATAAAAACTATCTCAAGTGAGATAAATTTTGTTTCGAGTGAAGCAATTTCAAAATTT
1 TGATTTTAAGAAAAACCATCTCAAATGAGATAAATTTTGTTTCGAGTGAAACAATTTCAAAATTT
* * * *
1302768 GTCTTTCAAGGGAAAACTGCATCAAGCGAGATGAAACTTATTTTAAGAAAAACCATCTCAAATGA
66 CTCTTTCAAGGGAAAACTGCATCAAGCGAGATGAAACTGATTTAAAGAAAAACCATCCCAAATGA
* *
1302833 GATAAATTTTTGTTTCGAGTGAAAGAATTTCAAAATTTGTGTTTCAAGGGAAAACTGCATCAA
131 GATAAATTTTTGTTT-AAGTGAAACAATTTCAAAATTT-TGTTTCAAGGGAAAACTGCATCAA
*
1302896 TGATTTTAAGAAAAACCATCTCAAATGAGATAAATTTTTGTTTCGAGTGAAATAATTTCAAAATT
1 TGATTTTAAGAAAAACCATCTCAAATGAGATAAA-TTTTGTTTCGAGTGAAACAATTTCAAAATT
* * * *
1302961 TCTGTTTCAAGGGAAAACTATC-TCAAGTGAGATGAAACTGATTTAAAGAAAAACCATCCCAAGT
65 TCTCTTTCAAGGGAAAACT-GCATCAAGCGAGATGAAACTGATTTAAAGAAAAACCATCCCAAAT
* *
1303025 GAGATAAATTTTTGTTTAAGTGAAACAATTTTAGAATTTTGTTTCAAGGGAAAACT
129 GAGATAAATTTTTGTTTAAGTGAAACAATTTCAAAATTTTGTTTCAAGGGAAAACT
1303081 ATCTCAAGCG
Statistics
Matches: 166, Mismatches: 17, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
192 17 0.10
193 49 0.30
194 99 0.60
195 1 0.01
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.33
Consensus pattern (191 bp):
TGATTTTAAGAAAAACCATCTCAAATGAGATAAATTTTGTTTCGAGTGAAACAATTTCAAAATTT
CTCTTTCAAGGGAAAACTGCATCAAGCGAGATGAAACTGATTTAAAGAAAAACCATCCCAAATGA
GATAAATTTTTGTTTAAGTGAAACAATTTCAAAATTTTGTTTCAAGGGAAAACTGCATCAA
Found at i:1306526 original size:64 final size:64
Alignment explanation
Indices: 1306456--1306591 Score: 263
Period size: 64 Copynumber: 2.1 Consensus size: 64
1306446 GTGTGCATTA
1306456 ATGCACTACCTGTGCATCGATACACAAATCACCTTCGATGTTATATTCTTAAGGGGATGCATCG
1 ATGCACTACCTGTGCATCGATACACAAATCACCTTCGATGTTATATTCTTAAGGGGATGCATCG
*
1306520 ATGCACTACCTGTGCATCGATACACAAATCACCTTCGATGTTTTATTCTTAAGGGGATGCATCG
1 ATGCACTACCTGTGCATCGATACACAAATCACCTTCGATGTTATATTCTTAAGGGGATGCATCG
1306584 ATGCACTA
1 ATGCACTA
1306592 ATTGCATTTG
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
64 71 1.00
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (64 bp):
ATGCACTACCTGTGCATCGATACACAAATCACCTTCGATGTTATATTCTTAAGGGGATGCATCG
Found at i:1306645 original size:21 final size:22
Alignment explanation
Indices: 1306616--1306656 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1306606 TCATTTATTT
1306616 AAGAGTGCATCGATACACATTG
1 AAGAGTGCATCGATACACATTG
*
1306638 AAGA-TGCATCGATGCACAT
1 AAGAGTGCATCGATACACAT
1306657 AACCCAGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.22
Consensus pattern (22 bp):
AAGAGTGCATCGATACACATTG
Found at i:1309051 original size:10 final size:10
Alignment explanation
Indices: 1309034--1309063 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
1309024 TTTTTTTTTT
1309034 CAAAAAAAAGG
1 CAAAAAAAA-G
1309045 CAAAAAAAAG
1 CAAAAAAAAG
1309055 CAAAAAAAA
1 CAAAAAAAA
1309064 ACCAAAAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.80, C:0.10, G:0.10, T:0.00
Consensus pattern (10 bp):
CAAAAAAAAG
Found at i:1309070 original size:10 final size:11
Alignment explanation
Indices: 1309034--1309072 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
1309024 TTTTTTTTTT
*
1309034 CAAAAAAAAGG
1 CAAAAAAAAGC
1309045 CAAAAAAAAG-
1 CAAAAAAAAGC
*
1309055 CAAAAAAAAAC
1 CAAAAAAAAGC
1309066 CAAAAAA
1 CAAAAAA
1309073 GCCAAAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
10 9 0.35
11 17 0.65
ACGTcount: A:0.79, C:0.13, G:0.08, T:0.00
Consensus pattern (11 bp):
CAAAAAAAAGC
Found at i:1314406 original size:24 final size:25
Alignment explanation
Indices: 1314358--1314407 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
1314348 TCTTTTGATA
1314358 TTTCAGATTCGAGGACGAATCCTTT
1 TTTCAGATTCGAGGACGAATCCTTT
*
1314383 TTTCAGATTCGAGG-GGAATCCTTT
1 TTTCAGATTCGAGGACGAATCCTTT
1314407 T
1 T
1314408 AAGGAAGGGG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 10 0.42
25 14 0.58
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (25 bp):
TTTCAGATTCGAGGACGAATCCTTT
Done.