Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000349.1 Hibiscus syriacus cultivar Beakdansim tig00000643_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: 88862
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:837 original size:6 final size:6
Alignment explanation
Indices: 826--857 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
816 CATTAAAGGA
826 GAGAGG GAGA-G G-GAGG GAGAGG GAGAGG GAGA
1 GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGA
858 AAGGGTCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
4 2 0.08
5 4 0.17
6 18 0.75
ACGTcount: A:0.34, C:0.00, G:0.66, T:0.00
Consensus pattern (6 bp):
GAGAGG
Found at i:847 original size:16 final size:16
Alignment explanation
Indices: 826--856 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
816 CATTAAAGGA
826 GAGAGGGAGAGGGAGG
1 GAGAGGGAGAGGGAGG
842 GAGAGGGAGAGGGAG
1 GAGAGGGAGAGGGAG
857 AAAGGGTCAA
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:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (16 bp):
GAGAGGGAGAGGGAGG
Found at i:13386 original size:26 final size:26
Alignment explanation
Indices: 13350--13403 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
13340 CAAGTTAGGC
13350 TTATGGTTCTGATTACAGATGATCCG
1 TTATGGTTCTGATTACAGATGATCCG
13376 TTATGGTTCTGATTACAGATGATCCG
1 TTATGGTTCTGATTACAGATGATCCG
13402 TT
1 TT
13404 GGAATCAACC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.22, C:0.15, G:0.22, T:0.41
Consensus pattern (26 bp):
TTATGGTTCTGATTACAGATGATCCG
Found at i:16988 original size:46 final size:46
Alignment explanation
Indices: 16912--17106 Score: 288
Period size: 46 Copynumber: 4.3 Consensus size: 46
16902 ATTTGCATAT
* * *
16912 CCAATAT-TTTACCATTTATTAACCATAAGCTCGTAAGTTTATTTTA
1 CCAATATACTTACCATTTAAT-ACCATAAGCTCGTAAGCTTATTTTA
* *
16958 TCAAAATACTTACCATTTAATACCATAAGCTCGTAAGCTTATTTTA
1 CCAATATACTTACCATTTAATACCATAAGCTCGTAAGCTTATTTTA
* *
17004 CCAATATACTTACTATTTAATACCATAAGCTCATAAGCTTATTTTA
1 CCAATATACTTACCATTTAATACCATAAGCTCGTAAGCTTATTTTA
17050 CCAATATACTTACCATTT-AT-CCATAAGCTCGTAAGCTTATTTTA
1 CCAATATACTTACCATTTAATACCATAAGCTCGTAAGCTTATTTTA
*
17094 CCAATACACTTAC
1 CCAATATACTTAC
17107 TATTATTCCA
Statistics
Matches: 136, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
44 35 0.26
45 2 0.01
46 88 0.65
47 11 0.08
ACGTcount: A:0.35, C:0.21, G:0.06, T:0.38
Consensus pattern (46 bp):
CCAATATACTTACCATTTAATACCATAAGCTCGTAAGCTTATTTTA
Found at i:17105 original size:90 final size:92
Alignment explanation
Indices: 16933--17110 Score: 297
Period size: 90 Copynumber: 2.0 Consensus size: 92
16923 CCATTTATTA
* * *
16933 ACCATAAGCTCGTAAGTTTATTTTATCAAAATACTTACCATTTAATACCATAAGCTCGTAAGCTT
1 ACCATAAGCTCATAAGCTTATTTTACCAAAATACTTACCATTTAATACCATAAGCTCGTAAGCTT
*
16998 ATTTTACCAATATACTTACTATTTAAT
66 ATTTTACCAATACACTTACTATTTAAT
*
17025 ACCATAAGCTCATAAGCTTATTTTACCAATATACTTACCATTT-AT-CCATAAGCTCGTAAGCTT
1 ACCATAAGCTCATAAGCTTATTTTACCAAAATACTTACCATTTAATACCATAAGCTCGTAAGCTT
17088 ATTTTACCAATACACTTACTATT
66 ATTTTACCAATACACTTACTATT
17111 ATTCCATAAC
Statistics
Matches: 81, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
90 40 0.49
91 2 0.02
92 39 0.48
ACGTcount: A:0.35, C:0.21, G:0.06, T:0.38
Consensus pattern (92 bp):
ACCATAAGCTCATAAGCTTATTTTACCAAAATACTTACCATTTAATACCATAAGCTCGTAAGCTT
ATTTTACCAATACACTTACTATTTAAT
Found at i:17321 original size:61 final size:61
Alignment explanation
Indices: 17205--17321 Score: 148
Period size: 61 Copynumber: 1.9 Consensus size: 61
17195 GCTAAACTTG
* * * *
17205 CACTAAGCTTACGTCATAGTGTTAATCCGGACAATACACATAAGGTCGTGCCCACCACCTA
1 CACTAAGCTTACGTCATAGTGCTAATCCAGACAATACACATAAGATCGTACCCACCACCTA
* *
17266 CACTAAGCTTACG-CTATAGTGCTAATCCAGAC-ATGATACATAAGATCGTATCCACC
1 CACTAAGCTTACGTC-ATAGTGCTAATCCAGACAAT-ACACATAAGATCGTACCCACC
17322 TTTCCCGCAC
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
60 3 0.06
61 45 0.94
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.24
Consensus pattern (61 bp):
CACTAAGCTTACGTCATAGTGCTAATCCAGACAATACACATAAGATCGTACCCACCACCTA
Found at i:21269 original size:21 final size:21
Alignment explanation
Indices: 21243--21289 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
21233 GATTCGTAAC
21243 GCGAACTTCGACTATCGCAAT
1 GCGAACTTCGACTATCGCAAT
* *
21264 GCGAACTTGGACTGTCGCAAT
1 GCGAACTTCGACTATCGCAAT
*
21285 ACGAA
1 GCGAA
21290 TATGTAAATC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.30, C:0.26, G:0.23, T:0.21
Consensus pattern (21 bp):
GCGAACTTCGACTATCGCAAT
Found at i:21328 original size:21 final size:21
Alignment explanation
Indices: 21298--21385 Score: 115
Period size: 21 Copynumber: 4.2 Consensus size: 21
21288 AATATGTAAA
*
21298 TCGCAATGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCGAAGT
*
21319 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCGAAGT
* *
21340 TCGTATTGCGATAGTCG-ACT
1 TCGCATTGCGATAGTCGAAGT
*
21360 ATCGTATTGCGATAGTCGAAGT
1 -TCGCATTGCGATAGTCGAAGT
21382 TCGC
1 TCGC
21386 GTTGTGATTT
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
20 2 0.03
21 54 0.93
22 2 0.03
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (21 bp):
TCGCATTGCGATAGTCGAAGT
Found at i:21522 original size:6 final size:6
Alignment explanation
Indices: 21511--21552 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
21501 GACACGTATT
21511 ACCACG ACCACG ACCACG ACC-CG ACC-CG ACCACG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
21553 CGAGACGGAC
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
5 15 0.43
6 20 0.57
ACGTcount: A:0.29, C:0.55, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:21537 original size:5 final size:5
Alignment explanation
Indices: 21515--21555 Score: 55
Period size: 5 Copynumber: 7.6 Consensus size: 5
21505 CGTATTACCA
21515 CGACC ACGACC ACGACC CGACC CGACC ACGACC CGACC CGA
1 CGACC -CGACC -CGACC CGACC CGACC -CGACC CGACC CGA
21556 GACGGACGGC
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
5 18 0.53
6 16 0.47
ACGTcount: A:0.27, C:0.54, G:0.20, T:0.00
Consensus pattern (5 bp):
CGACC
Found at i:21540 original size:16 final size:16
Alignment explanation
Indices: 21515--21555 Score: 73
Period size: 16 Copynumber: 2.5 Consensus size: 16
21505 CGTATTACCA
21515 CGACCACGACCACGACC
1 CGACC-CGACCACGACC
21532 CGACCCGACCACGACC
1 CGACCCGACCACGACC
21548 CGACCCGA
1 CGACCCGA
21556 GACGGACGGC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 19 0.79
17 5 0.21
ACGTcount: A:0.27, C:0.54, G:0.20, T:0.00
Consensus pattern (16 bp):
CGACCCGACCACGACC
Found at i:21546 original size:11 final size:11
Alignment explanation
Indices: 21515--21552 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
21505 CGTATTACCA
21515 CGACCACGACC
1 CGACCACGACC
21526 ACGACC-CGACC
1 -CGACCACGACC
21537 CGACCACGACC
1 CGACCACGACC
21548 CGACC
1 CGACC
21553 CGAGACGGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 5 0.20
11 15 0.60
12 5 0.20
ACGTcount: A:0.26, C:0.55, G:0.18, T:0.00
Consensus pattern (11 bp):
CGACCACGACC
Found at i:22214 original size:21 final size:20
Alignment explanation
Indices: 22162--22223 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 20
22152 CGTTGCGATT
22162 TTGGACTATCGCAA-CGAAC
1 TTGGACTATCGCAAGCGAAC
*
22181 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAA-GCGAAC
22204 TTGGACTATCGCAATGCGAA
1 TTGGACTATCGCAA-GCGAA
22224 TATGTAAATC
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
19 6 0.17
21 19 0.53
23 11 0.31
ACGTcount: A:0.34, C:0.23, G:0.23, T:0.21
Consensus pattern (20 bp):
TTGGACTATCGCAAGCGAAC
Found at i:22766 original size:2 final size:2
Alignment explanation
Indices: 22759--22801 Score: 50
Period size: 2 Copynumber: 21.5 Consensus size: 2
22749 GCAGTTTTGG
* * * *
22759 TA TA TA TA TA TA TA TA TA CA TA TG TA TG TA TG 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
22801 T
1 T
22802 GTATGTATGT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.49
Consensus pattern (2 bp):
TA
Found at i:22806 original size:4 final size:4
Alignment explanation
Indices: 22779--22813 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
22769 TATATATACA
* *
22779 TATG TATG TATG TATA TATA TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TAT
22814 TTATATTCCC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.17, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:22818 original size:20 final size:20
Alignment explanation
Indices: 22771--22819 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
22761 TATATATATA
*
22771 TATATACATATGTATGTATG
1 TATATATATATGTATGTATG
22791 TATATATATATGTATGTATG
1 TATATATATATGTATGTATG
*
22811 TATTTATAT
1 TATATATAT
22820 TCCCATAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.35, C:0.02, G:0.12, T:0.51
Consensus pattern (20 bp):
TATATATATATGTATGTATG
Found at i:31186 original size:6 final size:6
Alignment explanation
Indices: 31175--31215 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
31165 TTTTATACCA
* *
31175 CCATCT CCATCT CCATCT CCATCT CCATCA CCATCA CCATC
1 CCATCT CCATCT CCATCT CCATCT CCATCT CCATCT CCATC
31216 GTATCTTCCG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.22, C:0.51, G:0.00, T:0.27
Consensus pattern (6 bp):
CCATCT
Found at i:31387 original size:2 final size:2
Alignment explanation
Indices: 31380--31405 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
31370 GTGTGATTCC
31380 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
31406 TCATTTCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:32004 original size:2 final size:2
Alignment explanation
Indices: 31997--32030 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
31987 GTGTGATTCC
31997 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
32031 TCATTTCTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:42051 original size:31 final size:31
Alignment explanation
Indices: 42015--42075 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
42005 AACTTAAAAG
* *
42015 AGTTTTGCAATACTGATATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
42046 AGTTTTACAATACTGAAATTTAAATAATTT
1 AGTTTTACAATACTGAAATTTAAATAATTT
42076 ATACAACTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.39, C:0.07, G:0.08, T:0.46
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:42554 original size:19 final size:19
Alignment explanation
Indices: 42532--42584 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 19
42522 TATTTAAACT
42532 TAAATCAAAATAATTAA-AA
1 TAAAT-AAAATAATTAATAA
42551 TAAATATAAA-ATATTAATAA
1 TAAATA-AAATA-ATTAATAA
*
42571 TATATAAAATAATT
1 TAAATAAAATAATT
42585 TGTATGATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
18 2 0.07
19 19 0.66
20 8 0.28
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (19 bp):
TAAATAAAATAATTAATAA
Found at i:42871 original size:44 final size:39
Alignment explanation
Indices: 42801--42888 Score: 124
Period size: 44 Copynumber: 2.2 Consensus size: 39
42791 ACTATCTCAA
42801 TGCGA-TTTTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
1 TGCGATTTTTCCAAATTCGTTGCGATAGTCCAAGTT--CGT
42841 TGCGATTTATTCCAAATTCGCGTTGCGATAGTCCAAGTTCGT
1 TGCGATTT-TTCCAAATT--CGTTGCGATAGTCCAAGTTCGT
42883 TGCGAT
1 TGCGAT
42889 AGTCGAAGTT
Statistics
Matches: 44, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
40 5 0.11
41 2 0.05
42 18 0.41
44 19 0.43
ACGTcount: A:0.20, C:0.22, G:0.23, T:0.35
Consensus pattern (39 bp):
TGCGATTTTTCCAAATTCGTTGCGATAGTCCAAGTTCGT
Found at i:42918 original size:42 final size:42
Alignment explanation
Indices: 42857--43102 Score: 415
Period size: 42 Copynumber: 5.9 Consensus size: 42
42847 TTATTCCAAA
*
42857 TTCGCGTTGCGA--TAGTCCAAGTTCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAG
*
42897 TTCACGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAG
* *
42939 TTTGCGTTGCGATTTATTTCAAGTTCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAG
* *
42981 TTCGCGTTGCGATTTATTCCAAATTCGTTGAGATAGTCGAAG
1 TTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAG
*
43023 TTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATATTCGAAG
1 TTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAG
43065 TTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTC
1 TTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTC
43103 CAAATCACAA
Statistics
Matches: 191, Mismatches: 13, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
40 11 0.06
42 180 0.94
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (42 bp):
TTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAG
Found at i:43205 original size:6 final size:6
Alignment explanation
Indices: 43194--43220 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
43184 GACACGTATT
43194 ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACC
43221 CGAGACGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.52, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:43886 original size:6 final size:6
Alignment explanation
Indices: 43866--43909 Score: 72
Period size: 6 Copynumber: 7.5 Consensus size: 6
43856 TCTCGTCTCG
*
43866 GGTCG- GGTCGT GGTCGA GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
43910 AATACGTGTC
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
5 5 0.14
6 31 0.86
ACGTcount: A:0.02, C:0.16, G:0.52, T:0.30
Consensus pattern (6 bp):
GGTCGT
Found at i:44064 original size:42 final size:41
Alignment explanation
Indices: 44002--44303 Score: 257
Period size: 42 Copynumber: 7.3 Consensus size: 41
43992 TGAGATTTTG
44002 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAAC-CGAACTTC
* * *
44044 GACTATCGCAATGAATTTGGAATAAATCG----CGAACTTT
1 GACTATCGCAACGAACTTGGAATAAATCGCAACCGAACTTC
* * *
44081 AACTATCGCAACGAACTTGGAATAAATCGCAA-CGAATTTA
1 GACTATCGCAACGAACTTGGAATAAATCGCAACCGAACTTC
* * * *
44121 GAATAAATCGCAACGCAAACTTCGACT--ATCGCAA-CGAACTTG
1 GACT--ATCGCAACG--AACTTGGAATAAATCGCAACCGAACTTC
* * * * *
44163 GAATAAATCGCAACGCGAACTTCGACT--ATCGCAA-CGAATTTG
1 GACT--ATCGCAA--CGAACTTGGAATAAATCGCAACCGAACTTC
*
44205 GAATAAATCGCAACGAACTTGGAATAAATCGCAACTCGAACTTC
1 GACT--ATCGCAACGAACTTGGAATAAATCGCAAC-CGAACTTC
*
44249 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAAC-CGAACTTC
44291 GACTATCGCAACG
1 GACTATCGCAACG
44304 CGATAGTCCA
Statistics
Matches: 225, Mismatches: 22, Indels: 26
0.82 0.08 0.10
Matches are distributed among these distances:
37 33 0.15
40 18 0.08
42 155 0.69
44 19 0.08
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.22
Consensus pattern (41 bp):
GACTATCGCAACGAACTTGGAATAAATCGCAACCGAACTTC
Found at i:44086 original size:37 final size:37
Alignment explanation
Indices: 44003--44110 Score: 135
Period size: 37 Copynumber: 2.8 Consensus size: 37
43993 GAGATTTTGG
*
44003 ACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCG
1 ACTATCGCAACGAACTTGGAATAAAT-----CGCGAACTTCA
* * *
44045 ACTATCGCAATGAATTTGGAATAAATCGCGAACTTTA
1 ACTATCGCAACGAACTTGGAATAAATCGCGAACTTCA
44082 ACTATCGCAACGAACTTGGAATAAATCGC
1 ACTATCGCAACGAACTTGGAATAAATCGC
44111 AACGAATTTA
Statistics
Matches: 60, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
37 36 0.60
42 24 0.40
ACGTcount: A:0.37, C:0.22, G:0.18, T:0.23
Consensus pattern (37 bp):
ACTATCGCAACGAACTTGGAATAAATCGCGAACTTCA
Found at i:44135 original size:21 final size:21
Alignment explanation
Indices: 44006--44073 Score: 68
Period size: 21 Copynumber: 3.2 Consensus size: 21
43996 ATTTTGGACT
44006 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
* *
44027 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAACTTGGAATAA
* *
44048 ATCGCAATGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
44069 ATCGC
1 ATCGC
44074 GAACTTTAAC
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
19 8 0.22
21 19 0.51
23 10 0.27
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (21 bp):
ATCGCAACGAACTTGGAATAA
Found at i:44151 original size:21 final size:21
Alignment explanation
Indices: 44105--44304 Score: 139
Period size: 21 Copynumber: 9.5 Consensus size: 21
44095 ACTTGGAATA
* *
44105 AATCGCAACG-AATTTAGAAT
1 AATCGCAACGCAACTTCGAAT
*
44125 AAATCGCAACGCAAACTTCGACT
1 -AATCGCAACGC-AACTTCGAAT
*
44148 -ATCGCAACG-AACTTGGAAT
1 AATCGCAACGCAACTTCGAAT
*
44167 AAATCGCAACGCGAACTTCGACT
1 -AATCGCAACGC-AACTTCGAAT
* *
44190 -ATCGCAACG-AATTTGGAAT
1 AATCGCAACGCAACTTCGAAT
*
44209 AAATCGCAACG-AACTTGGAAT
1 -AATCGCAACGCAACTTCGAAT
* *
44230 AAATCGCAACTCGAACTTCGACT
1 -AATCGCAACGC-AACTTCGAAT
* *
44253 -ATCGCAACG-AATTTGGAAT
1 AATCGCAACGCAACTTCGAAT
*
44272 AAATCGCAACGCGAACTTCGACT
1 -AATCGCAACGC-AACTTCGAAT
44295 -ATCGCAACGC
1 AATCGCAACGC
44305 GATAGTCCAA
Statistics
Matches: 144, Mismatches: 21, Indels: 28
0.75 0.11 0.15
Matches are distributed among these distances:
19 22 0.15
21 92 0.64
23 30 0.21
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.20
Consensus pattern (21 bp):
AATCGCAACGCAACTTCGAAT
Found at i:44214 original size:105 final size:105
Alignment explanation
Indices: 44006--44303 Score: 480
Period size: 105 Copynumber: 2.9 Consensus size: 105
43996 ATTTTGGACT
*
44006 ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAATGAATTTGGAATAAAT
1 ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAAAT
**
44071 -----CGCGAACTTTAACTATCGCAACGAACTTGGAATAA
66 CGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAA
* * * *
44106 ATCGCAACGAATTTAGAATAAATCGCAACGCAAACTTCGACTATCGCAACGAACTTGGAATAAAT
1 ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAAAT
*
44171 CGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAA
66 CGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAA
*
44211 ATCGCAACGAACTTGGAATAAATCGCAACTCGAACTTCGACTATCGCAACGAATTTGGAATAAAT
1 ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAAAT
44276 CGCAACGCGAACTTCGACTATCGCAACG
66 CGCAACGCGAACTTCGACTATCGCAACG
44304 CGATAGTCCA
Statistics
Matches: 180, Mismatches: 13, Indels: 5
0.91 0.07 0.03
Matches are distributed among these distances:
100 60 0.33
105 120 0.67
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.21
Consensus pattern (105 bp):
ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAAAT
CGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAA
Found at i:44264 original size:63 final size:62
Alignment explanation
Indices: 44085--44282 Score: 267
Period size: 63 Copynumber: 3.1 Consensus size: 62
44075 AACTTTAACT
* * * * * *
44085 ATCGCAACGAACTTGGAATAAATCGCAA-CGAATTTAGAATAAATCGCAACGCAAACTTCGACT-
1 ATCGCAACGAACTTGGAATAAATCGCAACCGAACTTCGACT--ATCGCAACG--AATTTGGAATA
44148 -
62 A
44148 ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAAATCGCAAC-CGAACTTCGACTATCGCAACGAATTTGGAATAA
44211 ATCGCAACGAACTTGGAATAAATCGCAACTCGAACTTCGACTATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAAATCGCAAC-CGAACTTCGACTATCGCAACGAATTTGGAATAA
44274 ATCGCAACG
1 ATCGCAACG
44283 CGAACTTCGA
Statistics
Matches: 124, Mismatches: 7, Indels: 8
0.89 0.05 0.06
Matches are distributed among these distances:
61 7 0.06
63 108 0.87
65 9 0.07
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.21
Consensus pattern (62 bp):
ATCGCAACGAACTTGGAATAAATCGCAACCGAACTTCGACTATCGCAACGAATTTGGAATAA
Found at i:44299 original size:63 final size:62
Alignment explanation
Indices: 44148--44306 Score: 239
Period size: 63 Copynumber: 2.5 Consensus size: 62
44138 AACTTCGACT
*
44148 ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTCGAAT-AATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAA
* *
44211 ATCGCAACGAACTTGGAATAAATCGCAACTCGAACTTCGACTATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTCGAAT-AATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAA
*
44274 ATCGCAACGCGAACTTCGACT-ATCGCAACGCGA
1 ATCGCAA--CGAACTTCGAATAATCGCAACGCGA
44307 TAGTCCAAGT
Statistics
Matches: 90, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
63 80 0.89
65 10 0.11
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.20
Consensus pattern (62 bp):
ATCGCAACGAACTTCGAATAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAA
Found at i:44514 original size:12 final size:12
Alignment explanation
Indices: 44476--44610 Score: 88
Period size: 12 Copynumber: 11.2 Consensus size: 12
44466 TTTTTCTTAA
44476 AAAATTAATATT
1 AAAATTAATATT
* *
44488 -TAATTTAT-TT
1 AAAATTAATATT
44498 AAAAATTAATATT
1 -AAAATTAATATT
44511 AAAATTAATATAT
1 AAAATTAATAT-T
*
44524 ATAATATAATATT
1 AAAAT-TAATATT
44537 AAAAAATTAATATT
1 --AAAATTAATATT
* *
44551 -TAATTTAT-TT
1 AAAATTAATATT
44561 AAAAATTAATATT
1 -AAAATTAATATT
*
44574 AAAATTAA-A-A
1 AAAATTAATATT
44584 ACAAATATAATA-T
1 A-AAAT-TAATATT
44597 AAAATTAA-ATT
1 AAAATTAATATT
44608 AAA
1 AAA
44611 TATAAAACCT
Statistics
Matches: 97, Mismatches: 12, Indels: 29
0.70 0.09 0.21
Matches are distributed among these distances:
10 6 0.06
11 24 0.25
12 38 0.39
13 12 0.12
14 13 0.13
15 4 0.04
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.41
Consensus pattern (12 bp):
AAAATTAATATT
Found at i:44534 original size:26 final size:24
Alignment explanation
Indices: 44501--44573 Score: 87
Period size: 23 Copynumber: 3.0 Consensus size: 24
44491 TTTATTTAAA
44501 AATTAATATT-AAAATTAATATATAT
1 AATTAATATTAAAAATTAATAT-T-T
44526 AATATAATATTAAAAAATTAATATTT
1 AAT-TAATATT-AAAAATTAATATTT
*
44552 AATTTAT-TTAAAAATTAATATT
1 AATTAATATTAAAAATTAATATT
44574 AAAATTAAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
23 13 0.30
24 2 0.05
25 6 0.14
26 11 0.25
27 1 0.02
28 11 0.25
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
AATTAATATTAAAAATTAATATTT
Found at i:44607 original size:63 final size:63
Alignment explanation
Indices: 44474--44609 Score: 213
Period size: 63 Copynumber: 2.2 Consensus size: 63
44464 ATTTTTTCTT
* * *
44474 AAAAAATTAATATTTAATTTATTTAAAAATTAATATTAAAATTAATATATATAATATAATATT
1 AAAAAATTAATATTTAATTTATTTAAAAATTAATATTAAAATTAATAAACATAATATAATATA
44537 AAAAAATTAATATTTAATTTATTTAAAAATTAATATTAAAATTAA-AAACA-AATATAATATA
1 AAAAAATTAATATTTAATTTATTTAAAAATTAATATTAAAATTAATAAACATAATATAATATA
44598 AAATTAAATTAA
1 AAA--AAATTAA
44610 ATATAAAACC
Statistics
Matches: 68, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
61 13 0.19
62 3 0.04
63 52 0.76
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (63 bp):
AAAAAATTAATATTTAATTTATTTAAAAATTAATATTAAAATTAATAAACATAATATAATATA
Found at i:45522 original size:3 final size:3
Alignment explanation
Indices: 45514--45539 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
45504 CGGGTGTCAA
45514 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
45540 ATACATTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:46383 original size:31 final size:30
Alignment explanation
Indices: 46348--46421 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 30
46338 GGGGCCGTGG
*
46348 GGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
46379 GGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGCCTACCTAAGAAACATCTCAGGGCCGCA
46409 GAGCCTACCTAAG
1 G-GCCTACCTAAG
46422 TGTCACATTA
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
30 14 0.40
31 21 0.60
ACGTcount: A:0.27, C:0.32, G:0.26, T:0.15
Consensus pattern (30 bp):
GGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:46416 original size:62 final size:63
Alignment explanation
Indices: 46300--46421 Score: 151
Period size: 62 Copynumber: 2.0 Consensus size: 63
46290 ACCTAAGGGA
* * ** *
46300 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
*
46363 ACATCTTAGGGCC-GCAG-GCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAG
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAG
46422 TGTCACATTA
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
61 1 0.02
62 35 0.69
63 15 0.29
ACGTcount: A:0.25, C:0.30, G:0.28, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:47931 original size:18 final size:18
Alignment explanation
Indices: 47908--47942 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
47898 TTCCATCCGG
*
47908 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
47926 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
47943 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:49252 original size:8 final size:8
Alignment explanation
Indices: 49222--49278 Score: 52
Period size: 8 Copynumber: 7.5 Consensus size: 8
49212 GGTCAACAAT
49222 GGTCAACG
1 GGTCAACG
49230 CCGGTCAAC-
1 --GGTCAACG
49239 GGTCAACG
1 GGTCAACG
49247 GGTCAAC-
1 GGTCAACG
*
49254 GGTCAATG
1 GGTCAACG
49262 GGT---CG
1 GGTCAACG
49267 GGTCAACG
1 GGTCAACG
49275 GGTC
1 GGTC
49279 GGGTCGGGTC
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
5 4 0.10
7 13 0.32
8 16 0.40
10 7 0.17
ACGTcount: A:0.21, C:0.26, G:0.37, T:0.16
Consensus pattern (8 bp):
GGTCAACG
Found at i:49252 original size:15 final size:15
Alignment explanation
Indices: 49222--49278 Score: 64
Period size: 15 Copynumber: 3.8 Consensus size: 15
49212 GGTCAACAAT
49222 GGTCAACGCCGGTCAAC
1 GGTCAACG--GGTCAAC
49239 GGTCAACGGGTCAAC
1 GGTCAACGGGTCAAC
* *
49254 GGTCAATGGGTC--G
1 GGTCAACGGGTCAAC
49267 GGTCAACGGGTC
1 GGTCAACGGGTC
49279 GGGTCGGGTC
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
13 11 0.30
15 18 0.49
17 8 0.22
ACGTcount: A:0.21, C:0.26, G:0.37, T:0.16
Consensus pattern (15 bp):
GGTCAACGGGTCAAC
Found at i:49272 original size:13 final size:13
Alignment explanation
Indices: 49239--49327 Score: 61
Period size: 13 Copynumber: 6.3 Consensus size: 13
49229 GCCGGTCAAC
*
49239 GGTCAACGGGTCAAC
1 GGTCAACGGGTC--G
*
49254 GGTCAATGGGTCG
1 GGTCAACGGGTCG
49267 GGTCAACGGGTCGGGTCG
1 GGTCAAC--G---GGTCG
*
49285 GGTCAACTGGTCG
1 GGTCAACGGGTCG
* *
49298 GATAAACGGGTCG
1 GGTCAACGGGTCG
*
49311 GGTAAACGGGTCG
1 GGTCAACGGGTCG
49324 GGTC
1 GGTC
49328 GGGTCGGGTT
Statistics
Matches: 60, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
13 36 0.60
15 12 0.20
18 12 0.20
ACGTcount: A:0.19, C:0.20, G:0.43, T:0.18
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:49284 original size:18 final size:18
Alignment explanation
Indices: 49261--49298 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
49251 AACGGTCAAT
49261 GGGTCGGGTCAACGGGTC
1 GGGTCGGGTCAACGGGTC
*
49279 GGGTCGGGTCAACTGGTC
1 GGGTCGGGTCAACGGGTC
49297 GG
1 GG
49299 ATAAACGGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.11, C:0.21, G:0.50, T:0.18
Consensus pattern (18 bp):
GGGTCGGGTCAACGGGTC
Found at i:49297 original size:31 final size:31
Alignment explanation
Indices: 49254--49313 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
49244 ACGGGTCAAC
* *
49254 GGTCAATGGGTCGGGTCAACGGGTCGGGTCG
1 GGTCAATGGGTCGGATAAACGGGTCGGGTCG
49285 GGTCAACT-GGTCGGATAAACGGGTCGGGT
1 GGTCAA-TGGGTCGGATAAACGGGTCGGGT
49314 AAACGGGTCG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 25 0.96
32 1 0.04
ACGTcount: A:0.17, C:0.18, G:0.45, T:0.20
Consensus pattern (31 bp):
GGTCAATGGGTCGGATAAACGGGTCGGGTCG
Found at i:51406 original size:31 final size:30
Alignment explanation
Indices: 51371--51444 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 30
51361 GGGGCCGTGG
*
51371 GGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
51402 GGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGCCTACCTAAGAAACATCTCAGGGCCGCA
51432 GAGCCTACCTAAG
1 G-GCCTACCTAAG
51445 TGTCACATTA
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
30 14 0.40
31 21 0.60
ACGTcount: A:0.27, C:0.32, G:0.26, T:0.15
Consensus pattern (30 bp):
GGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:52956 original size:18 final size:18
Alignment explanation
Indices: 52933--52967 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
52923 TTCCATCCGG
*
52933 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
52951 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
52968 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:54276 original size:8 final size:8
Alignment explanation
Indices: 54246--54302 Score: 52
Period size: 8 Copynumber: 7.5 Consensus size: 8
54236 GGTCAACAAT
54246 GGTCAACG
1 GGTCAACG
54254 CCGGTCAAC-
1 --GGTCAACG
54263 GGTCAACG
1 GGTCAACG
54271 GGTCAAC-
1 GGTCAACG
*
54278 GGTCAATG
1 GGTCAACG
54286 GGT---CG
1 GGTCAACG
54291 GGTCAACG
1 GGTCAACG
54299 GGTC
1 GGTC
54303 GGGTCGGGTC
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
5 4 0.10
7 13 0.32
8 16 0.40
10 7 0.17
ACGTcount: A:0.21, C:0.26, G:0.37, T:0.16
Consensus pattern (8 bp):
GGTCAACG
Found at i:54276 original size:15 final size:15
Alignment explanation
Indices: 54246--54302 Score: 64
Period size: 15 Copynumber: 3.8 Consensus size: 15
54236 GGTCAACAAT
54246 GGTCAACGCCGGTCAAC
1 GGTCAACG--GGTCAAC
54263 GGTCAACGGGTCAAC
1 GGTCAACGGGTCAAC
* *
54278 GGTCAATGGGTC--G
1 GGTCAACGGGTCAAC
54291 GGTCAACGGGTC
1 GGTCAACGGGTC
54303 GGGTCGGGTC
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
13 11 0.30
15 18 0.49
17 8 0.22
ACGTcount: A:0.21, C:0.26, G:0.37, T:0.16
Consensus pattern (15 bp):
GGTCAACGGGTCAAC
Found at i:54296 original size:13 final size:13
Alignment explanation
Indices: 54263--54351 Score: 61
Period size: 13 Copynumber: 6.3 Consensus size: 13
54253 GCCGGTCAAC
*
54263 GGTCAACGGGTCAAC
1 GGTCAACGGGTC--G
*
54278 GGTCAATGGGTCG
1 GGTCAACGGGTCG
54291 GGTCAACGGGTCGGGTCG
1 GGTCAAC--G---GGTCG
*
54309 GGTCAACTGGTCG
1 GGTCAACGGGTCG
* *
54322 GATAAACGGGTCG
1 GGTCAACGGGTCG
*
54335 GGTAAACGGGTCG
1 GGTCAACGGGTCG
54348 GGTC
1 GGTC
54352 GGGTCGGGTT
Statistics
Matches: 60, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
13 36 0.60
15 12 0.20
18 12 0.20
ACGTcount: A:0.19, C:0.20, G:0.43, T:0.18
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:54308 original size:18 final size:18
Alignment explanation
Indices: 54285--54322 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
54275 AACGGTCAAT
54285 GGGTCGGGTCAACGGGTC
1 GGGTCGGGTCAACGGGTC
*
54303 GGGTCGGGTCAACTGGTC
1 GGGTCGGGTCAACGGGTC
54321 GG
1 GG
54323 ATAAACGGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.11, C:0.21, G:0.50, T:0.18
Consensus pattern (18 bp):
GGGTCGGGTCAACGGGTC
Found at i:54321 original size:31 final size:31
Alignment explanation
Indices: 54278--54337 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
54268 ACGGGTCAAC
* *
54278 GGTCAATGGGTCGGGTCAACGGGTCGGGTCG
1 GGTCAATGGGTCGGATAAACGGGTCGGGTCG
54309 GGTCAACT-GGTCGGATAAACGGGTCGGGT
1 GGTCAA-TGGGTCGGATAAACGGGTCGGGT
54338 AAACGGGTCG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 25 0.96
32 1 0.04
ACGTcount: A:0.17, C:0.18, G:0.45, T:0.20
Consensus pattern (31 bp):
GGTCAATGGGTCGGATAAACGGGTCGGGTCG
Found at i:56834 original size:30 final size:30
Alignment explanation
Indices: 56800--56864 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 30
56790 ATATATGTGC
* *
56800 TATGTGATCCTATGAGA-ATATGAAAAGAGA
1 TATGTGAACATATGA-ATATATGAAAAGAGA
*
56830 TATGTGAACATATGAATTATATGAAAAGTGA
1 TATGTGAACATATGAA-TATATGAAAAGAGA
56861 TATG
1 TATG
56865 AATTACATGA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 1 0.03
30 13 0.43
31 16 0.53
ACGTcount: A:0.43, C:0.05, G:0.22, T:0.31
Consensus pattern (30 bp):
TATGTGAACATATGAATATATGAAAAGAGA
Found at i:56865 original size:21 final size:21
Alignment explanation
Indices: 56839--56878 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
56829 ATATGTGAAC
*
56839 ATATGAATTATATGAAAAGTG
1 ATATGAATTACATGAAAAGTG
56860 ATATGAATTACATGAAAAG
1 ATATGAATTACATGAAAAG
56879 AAGCTATATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.50, C:0.03, G:0.17, T:0.30
Consensus pattern (21 bp):
ATATGAATTACATGAAAAGTG
Found at i:59031 original size:21 final size:19
Alignment explanation
Indices: 59002--59043 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 19
58992 ATTCTGAGTA
59002 TGTAAAAGAAGATAAGAATTT
1 TGTAAAAG-A-ATAAGAATTT
*
59023 TGTATAAGAATAAGAATTT
1 TGTAAAAGAATAAGAATTT
59042 TG
1 TG
59044 GGCAATTCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 12 0.60
20 1 0.05
21 7 0.35
ACGTcount: A:0.48, C:0.00, G:0.19, T:0.33
Consensus pattern (19 bp):
TGTAAAAGAATAAGAATTT
Found at i:63221 original size:17 final size:18
Alignment explanation
Indices: 63201--63243 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
63191 TTTAAACTCA
63201 TTTATATTTTTAT-TTGT
1 TTTATATTTTTATGTTGT
*
63218 TTTATA-ATTTATGTTGT
1 TTTATATTTTTATGTTGT
*
63235 TTTAAATTT
1 TTTATATTT
63244 AATATTTAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
16 5 0.24
17 15 0.71
18 1 0.05
ACGTcount: A:0.23, C:0.00, G:0.07, T:0.70
Consensus pattern (18 bp):
TTTATATTTTTATGTTGT
Found at i:63242 original size:16 final size:16
Alignment explanation
Indices: 63209--63244 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
63199 CATTTATATT
63209 TTTATTTGTTTTATAA
1 TTTATTTGTTTTATAA
63225 TTTATGTTGTTTTA-AA
1 TTTAT-TTGTTTTATAA
63241 TTTA
1 TTTA
63245 ATATTTAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.25, C:0.00, G:0.08, T:0.67
Consensus pattern (16 bp):
TTTATTTGTTTTATAA
Found at i:63665 original size:21 final size:21
Alignment explanation
Indices: 63639--63713 Score: 82
Period size: 21 Copynumber: 3.6 Consensus size: 21
63629 GCGTTGCATT
63639 TCGCGTTGCGATAGTCTACAG
1 TCGCGTTGCGATAGTCTACAG
* * *
63660 TCGCGTTGCGAT--TTTCCATT
1 TCGCGTTGCGATAGTCTACA-G
63680 TCGCGTTGCGATAGTCTACAG
1 TCGCGTTGCGATAGTCTACAG
*
63701 TTGTCGTTGCGAT
1 TCG-CGTTGCGAT
63714 TTTTCAAATT
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
19 4 0.09
20 12 0.28
21 14 0.33
22 13 0.30
ACGTcount: A:0.15, C:0.23, G:0.27, T:0.36
Consensus pattern (21 bp):
TCGCGTTGCGATAGTCTACAG
Found at i:63682 original size:41 final size:42
Alignment explanation
Indices: 63635--63716 Score: 148
Period size: 41 Copynumber: 2.0 Consensus size: 42
63625 AATCGCGTTG
63635 CATTTCGCGTTGCGATAGTCTACAGTCG-CGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTCTACAGTCGTCGTTGCGATTTTC
*
63676 CATTTCGCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTT
1 CATTTCGCGTTGCGATAGTCTACAGTCGTCGTTGCGATTTT
63717 TCAAATTCGT
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
41 27 0.69
42 12 0.31
ACGTcount: A:0.15, C:0.22, G:0.24, T:0.39
Consensus pattern (42 bp):
CATTTCGCGTTGCGATAGTCTACAGTCGTCGTTGCGATTTTC
Found at i:63728 original size:41 final size:40
Alignment explanation
Indices: 63642--63735 Score: 118
Period size: 41 Copynumber: 2.3 Consensus size: 40
63632 TTGCATTTCG
* *
63642 CGTTGCGATAGTCTACAGTCGCGTTGCGATTTTCCATTTC
1 CGTTGCGATAGTCTACAGTCGCGTTGCGATTTTCAAATTC
*
63682 GCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTTCAAATT-
1 -CGTTGCGATAGTCTACAGTCG-CGTTGCGA-TTTTCAAATTC
*
63724 CGTTGTGATAGT
1 CGTTGCGATAGT
63736 TAAAAAAAAG
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
41 31 0.66
42 8 0.17
43 8 0.17
ACGTcount: A:0.17, C:0.19, G:0.24, T:0.39
Consensus pattern (40 bp):
CGTTGCGATAGTCTACAGTCGCGTTGCGATTTTCAAATTC
Found at i:63823 original size:6 final size:6
Alignment explanation
Indices: 63812--63881 Score: 105
Period size: 6 Copynumber: 12.5 Consensus size: 6
63802 GACACGTATC
63812 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC-CG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
63859 ACC-CG ACC-CG ACC-CG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACC
63882 CGAGACGAGA
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 25 0.39
6 39 0.61
ACGTcount: A:0.29, C:0.54, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:64374 original size:5 final size:5
Alignment explanation
Indices: 64360--64421 Score: 117
Period size: 5 Copynumber: 12.6 Consensus size: 5
64350 CCGCCGCCGC
64360 CGTC- CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT
1 CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT
64409 CGTCT CGTCT CGT
1 CGTCT CGTCT CGT
64422 GGTCGTGGTC
Statistics
Matches: 57, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
4 4 0.07
5 53 0.93
ACGTcount: A:0.00, C:0.40, G:0.21, T:0.39
Consensus pattern (5 bp):
CGTCT
Found at i:64429 original size:6 final size:6
Alignment explanation
Indices: 64418--64526 Score: 218
Period size: 6 Copynumber: 18.2 Consensus size: 6
64408 TCGTCTCGTC
64418 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
64466 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
64514 TCGTGG TCGTGG T
1 TCGTGG TCGTGG T
64527 AATACGTGTC
Statistics
Matches: 103, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 103 1.00
ACGTcount: A:0.00, C:0.17, G:0.50, T:0.34
Consensus pattern (6 bp):
TCGTGG
Found at i:64646 original size:20 final size:20
Alignment explanation
Indices: 64621--64781 Score: 162
Period size: 20 Copynumber: 7.9 Consensus size: 20
64611 GCAACGAATT
64621 TGGAAAATCGCAACGCGAAA
1 TGGAAAATCGCAACGCGAAA
*
64641 TGGAAAATCGCAACGCGAAT
1 TGGAAAATCGCAACGCGAAA
** *
64661 TTCAACTATCGCAACGCGAAA
1 TGGAA-AATCGCAACGCGAAA
*
64682 TGGAAAATCGCAACGCG-AC
1 TGGAAAATCGCAACGCGAAA
**
64701 TGTAGACTATCGCAACGCGAAA
1 TG--GAAAATCGCAACGCGAAA
**
64723 TGGAAAATCGCAACGCGATT
1 TGGAAAATCGCAACGCGAAA
**
64743 TTCAACAATCGCAACGCGAAA
1 TGGAA-AATCGCAACGCGAAA
* *
64764 TGGAAAACCACAACGCGA
1 TGGAAAATCGCAACGCGA
64782 TTTTCAACTA
Statistics
Matches: 112, Mismatches: 24, Indels: 10
0.77 0.16 0.07
Matches are distributed among these distances:
19 3 0.03
20 61 0.54
21 45 0.40
22 3 0.03
ACGTcount: A:0.40, C:0.24, G:0.22, T:0.14
Consensus pattern (20 bp):
TGGAAAATCGCAACGCGAAA
Found at i:64672 original size:41 final size:41
Alignment explanation
Indices: 64627--64806 Score: 290
Period size: 41 Copynumber: 4.4 Consensus size: 41
64617 AATTTGGAAA
*
64627 ATCGCAACGCGAAATGGAAAATCGCAACGCGAATTTCAACT
1 ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACT
* *
64668 ATCGCAACGCGAAATGGAAAATCGCAACGCGACTGT-AGACT
1 ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA-ACT
*
64709 ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACA
1 ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACT
* *
64750 ATCGCAACGCGAAATGGAAAACCACAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACT
64791 ATCGCAACGCGAAATG
1 ATCGCAACGCGAAATG
64807 CAACGCGAAT
Statistics
Matches: 129, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
40 1 0.01
41 127 0.98
42 1 0.01
ACGTcount: A:0.38, C:0.25, G:0.21, T:0.16
Consensus pattern (41 bp):
ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACT
Found at i:64673 original size:21 final size:21
Alignment explanation
Indices: 64626--64803 Score: 123
Period size: 20 Copynumber: 8.7 Consensus size: 21
64616 GAATTTGGAA
* **
64626 AATCGCAACGCGAAATGGAA-
1 AATCGCAACGCGAATTTCAAC
64646 AATCGCAACGCGAATTTCAAC
1 AATCGCAACGCGAATTTCAAC
* * **
64667 TATCGCAACGCGAAATGGAA-
1 AATCGCAACGCGAATTTCAAC
* *
64687 AATCGCAACGCGACTGT-AGAC
1 AATCGCAACGCGAATTTCA-AC
* * **
64708 TATCGCAACGCGAAATGGAA-
1 AATCGCAACGCGAATTTCAAC
*
64728 AATCGCAACGCGATTTTCAAC
1 AATCGCAACGCGAATTTCAAC
* **
64749 AATCGCAACGCGAAATGGAA-
1 AATCGCAACGCGAATTTCAAC
* * *
64769 AACCACAACGCGATTTTCAAC
1 AATCGCAACGCGAATTTCAAC
*
64790 TATCGCAACGCGAA
1 AATCGCAACGCGAA
64804 ATGCAACGCG
Statistics
Matches: 116, Mismatches: 36, Indels: 11
0.71 0.22 0.07
Matches are distributed among these distances:
19 1 0.01
20 59 0.51
21 55 0.47
22 1 0.01
ACGTcount: A:0.39, C:0.25, G:0.20, T:0.16
Consensus pattern (21 bp):
AATCGCAACGCGAATTTCAAC
Found at i:64810 original size:21 final size:21
Alignment explanation
Indices: 64626--64810 Score: 155
Period size: 21 Copynumber: 9.0 Consensus size: 21
64616 GAATTTGGAA
*
64626 AATCGCAACGCGAAATGGAA-
1 AATCGCAACGCGAAATGCAAC
* *
64646 AATCGCAACGCGAATTTCAAC
1 AATCGCAACGCGAAATGCAAC
* *
64667 TATCGCAACGCGAAATGGAA-
1 AATCGCAACGCGAAATGCAAC
* *
64687 AATCGCAACGCG-ACTGTAGAC
1 AATCGCAACGCGAAATGCA-AC
* *
64708 TATCGCAACGCGAAATGGAA-
1 AATCGCAACGCGAAATGCAAC
** *
64728 AATCGCAACGCGATTTTCAAC
1 AATCGCAACGCGAAATGCAAC
*
64749 AATCGCAACGCGAAATGGAA-
1 AATCGCAACGCGAAATGCAAC
* * ** *
64769 AACCACAACGCGATTTTCAAC
1 AATCGCAACGCGAAATGCAAC
*
64790 TATCGCAACGCGAAATGCAAC
1 AATCGCAACGCGAAATGCAAC
64811 GCGAATTTGC
Statistics
Matches: 125, Mismatches: 34, Indels: 11
0.74 0.20 0.06
Matches are distributed among these distances:
19 4 0.03
20 58 0.46
21 59 0.47
22 4 0.03
ACGTcount: A:0.39, C:0.25, G:0.20, T:0.16
Consensus pattern (21 bp):
AATCGCAACGCGAAATGCAAC
Found at i:64897 original size:21 final size:21
Alignment explanation
Indices: 64871--64961 Score: 103
Period size: 21 Copynumber: 4.3 Consensus size: 21
64861 GAAATGGAAA
64871 ATCGCAACGCGATCTCCAACT
1 ATCGCAACGCGATCTCCAACT
** ** *
64892 ATCGCAACGCGAAAATGGAA-A
1 ATCGCAACGCG-ATCTCCAACT
64913 ATCGCAACGCGATCTCCAACT
1 ATCGCAACGCGATCTCCAACT
* *
64934 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATCTCCAACT
64955 ATCGCAA
1 ATCGCAA
64962 TGTGAAATGC
Statistics
Matches: 56, Mismatches: 12, Indels: 4
0.78 0.17 0.06
Matches are distributed among these distances:
20 4 0.07
21 48 0.86
22 4 0.07
ACGTcount: A:0.34, C:0.31, G:0.16, T:0.19
Consensus pattern (21 bp):
ATCGCAACGCGATCTCCAACT
Found at i:64921 original size:42 final size:42
Alignment explanation
Indices: 64846--64945 Score: 193
Period size: 42 Copynumber: 2.4 Consensus size: 42
64836 GTTGCGATTT
64846 CAACTATCGCAACGCG-AAATGGAAAATCGCAACGCGATCTC
1 CAACTATCGCAACGCGAAAATGGAAAATCGCAACGCGATCTC
64887 CAACTATCGCAACGCGAAAATGGAAAATCGCAACGCGATCTC
1 CAACTATCGCAACGCGAAAATGGAAAATCGCAACGCGATCTC
64929 CAACTATCGCAACGCGA
1 CAACTATCGCAACGCGA
64946 TTTTCAACTA
Statistics
Matches: 58, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 16 0.28
42 42 0.72
ACGTcount: A:0.37, C:0.30, G:0.19, T:0.14
Consensus pattern (42 bp):
CAACTATCGCAACGCGAAAATGGAAAATCGCAACGCGATCTC
Found at i:65506 original size:20 final size:20
Alignment explanation
Indices: 65481--65520 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
65471 TTTAATTTAA
65481 CATATTTAATGACCGTTAGG
1 CATATTTAATGACCGTTAGG
65501 CATATTTAATGACCGTTAGG
1 CATATTTAATGACCGTTAGG
65521 GGTAAGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (20 bp):
CATATTTAATGACCGTTAGG
Found at i:68966 original size:2 final size:2
Alignment explanation
Indices: 68961--68987 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
68951 CATTAAAAAA
68961 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
68988 CATAAAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:69088 original size:18 final size:18
Alignment explanation
Indices: 69035--69089 Score: 60
Period size: 17 Copynumber: 3.1 Consensus size: 18
69025 TATATCAGTT
69035 TAAACTATAATAAAATATA
1 TAAA-TATAATAAAATATA
* *
69054 -AAAAAAAATAAAA-ATA
1 TAAATATAATAAAATATA
*
69070 TAATTATAATAAAATATA
1 TAAATATAATAAAATATA
69088 TA
1 TA
69090 TCTTTAAGAT
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
16 3 0.10
17 18 0.62
18 8 0.28
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (18 bp):
TAAATATAATAAAATATA
Found at i:70328 original size:60 final size:60
Alignment explanation
Indices: 70221--70353 Score: 148
Period size: 60 Copynumber: 2.2 Consensus size: 60
70211 GTAGAGTGAC
* * *
70221 CATTTTGTAAC-TTTAATAGTCGAGTGACTCAACAAAGCAACTCCCTATAGTTTAAGGAT
1 CATTTTGTAACTTTTAATAGTCAAGAGACTCAACAAAGCAACTCCCTATAGTTGAAGGAT
* * * *
70280 CATTTTGTAACTTTTAATAGTTAAGAGACTCAATAAAGTCTTA-T-CCTATAGTTGAGGGAT
1 CATTTTGTAACTTTTAATAGTCAAGAGACTCAACAAAG-C-AACTCCCTATAGTTGAAGGAT
70340 CATTTGTGT-ACTTT
1 CATTT-TGTAACTTT
70354 ACCCTAAATT
Statistics
Matches: 63, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
59 11 0.17
60 46 0.73
61 5 0.08
62 1 0.02
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.38
Consensus pattern (60 bp):
CATTTTGTAACTTTTAATAGTCAAGAGACTCAACAAAGCAACTCCCTATAGTTGAAGGAT
Found at i:82017 original size:26 final size:25
Alignment explanation
Indices: 81981--82030 Score: 82
Period size: 26 Copynumber: 2.0 Consensus size: 25
81971 CTTTTGTTCA
*
81981 TATGGAATTCATGTTTCATGTACATG
1 TATGGAATTCATG-TACATGTACATG
82007 TATGGAATTCATGTACATGTACAT
1 TATGGAATTCATGTACATGTACAT
82031 ATACATATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 10 0.43
26 13 0.57
ACGTcount: A:0.30, C:0.12, G:0.18, T:0.40
Consensus pattern (25 bp):
TATGGAATTCATGTACATGTACATG
Done.