Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007403.1 Hibiscus syriacus cultivar Beakdansim tig00019996_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: 68220
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Found at i:731 original size:60 final size:60
Alignment explanation
Indices: 571--748 Score: 281
Period size: 60 Copynumber: 3.0 Consensus size: 60
561 CAGATAACCA
* * * * *
571 AATTCAAGGTTTTTTTTTTTAAGTAGTGCACC-AAATC-AGCATTTTAAACGAGGTGTAG
1 AATTCAAGCTTTTTTTATTCAACTAATGCACCAAAATCAAGCATTTTAAACGAGGTGTAG
629 AATTCAAGC-TTTTTTATTCAACTAATGCACCAAAATCAAGCATTTTAAACGAGGTGTAG
1 AATTCAAGCTTTTTTTATTCAACTAATGCACCAAAATCAAGCATTTTAAACGAGGTGTAG
*
688 AATTCAAGCTTTTTTTATTCAACTAATGCACCAAAATCAAGCATTTTAAAGGAGGTGTAG
1 AATTCAAGCTTTTTTTATTCAACTAATGCACCAAAATCAAGCATTTTAAACGAGGTGTAG
748 A
1 A
749 CCCGTCAGAC
Statistics
Matches: 111, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
57 18 0.16
58 13 0.12
59 30 0.27
60 50 0.45
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (60 bp):
AATTCAAGCTTTTTTTATTCAACTAATGCACCAAAATCAAGCATTTTAAACGAGGTGTAG
Found at i:965 original size:17 final size:18
Alignment explanation
Indices: 931--965 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
921 CACGGAATGT
931 AAGATTACCAGTGGAATA
1 AAGATTACCAGTGGAATA
949 AAGATTACCAG-GGAATA
1 AAGATTACCAGTGGAATA
966 TGCTTACGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.46, C:0.11, G:0.23, T:0.20
Consensus pattern (18 bp):
AAGATTACCAGTGGAATA
Found at i:2991 original size:21 final size:21
Alignment explanation
Indices: 2962--3015 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
2952 TGGTTCGTCG
* *
2962 TATGCTGGTGGAGTAGGTTCA
1 TATGGTGGTGGAGTAGGGTCA
*
2983 TATGGTGGTGGATTAGGGTCA
1 TATGGTGGTGGAGTAGGGTCA
*
3004 TATGGCGGTGGA
1 TATGGTGGTGGA
3016 TTGTATGGCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.19, C:0.07, G:0.43, T:0.31
Consensus pattern (21 bp):
TATGGTGGTGGAGTAGGGTCA
Found at i:3016 original size:21 final size:21
Alignment explanation
Indices: 2968--3017 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
2958 GTCGTATGCT
* * *
2968 GGTGGAGTAGGTTCATATGGT
1 GGTGGATTAGGGTCATATGGC
2989 GGTGGATTAGGGTCATATGGC
1 GGTGGATTAGGGTCATATGGC
3010 GGTGGATT
1 GGTGGATT
3018 GTATGGCAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.18, C:0.06, G:0.44, T:0.32
Consensus pattern (21 bp):
GGTGGATTAGGGTCATATGGC
Found at i:4584 original size:24 final size:25
Alignment explanation
Indices: 4553--4601 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
4543 TTTTCTTTTA
4553 AAAACAA-GGAAGTCACAGTGATCT
1 AAAACAAGGGAAGTCACAGTGATCT
*
4577 AAAACAAGGGAAGTTACAGTGATCT
1 AAAACAAGGGAAGTCACAGTGATCT
4602 TTGGTGAGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 7 0.30
25 16 0.70
ACGTcount: A:0.45, C:0.14, G:0.22, T:0.18
Consensus pattern (25 bp):
AAAACAAGGGAAGTCACAGTGATCT
Found at i:4679 original size:10 final size:11
Alignment explanation
Indices: 4659--4692 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
4649 TTATTTTATC
4659 ATTTAAATTTT
1 ATTTAAATTTT
*
4670 ATTTAATTTTT
1 ATTTAAATTTT
*
4681 AGTTAAATTTT
1 ATTTAAATTTT
4692 A
1 A
4693 GAAAAATTGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (11 bp):
ATTTAAATTTT
Found at i:4867 original size:15 final size:16
Alignment explanation
Indices: 4847--4883 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
4837 TGTTAAAATT
4847 TTAATTATTTTA-AAG
1 TTAATTATTTTATAAG
*
4862 TTAATTATTTTATAAT
1 TTAATTATTTTATAAG
4878 TTAATT
1 TTAATT
4884 TGTTTCGAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (16 bp):
TTAATTATTTTATAAG
Found at i:4935 original size:2 final size:2
Alignment explanation
Indices: 4928--5004 Score: 147
Period size: 2 Copynumber: 39.0 Consensus size: 2
4918 TTATGGGAAT
4928 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
4970 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5005 AATTTATGAA
Statistics
Matches: 74, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 73 0.99
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:11710 original size:14 final size:14
Alignment explanation
Indices: 11691--11730 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
11681 CAAAGTCAAT
**
11691 GAGTTGACTTGGAC
1 GAGTTGACTCAGAC
*
11705 GAGTTGACTCAGAT
1 GAGTTGACTCAGAC
11719 GAGTTGACTCAG
1 GAGTTGACTCAG
11731 TCCAGGTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.25, C:0.15, G:0.33, T:0.28
Consensus pattern (14 bp):
GAGTTGACTCAGAC
Found at i:14222 original size:19 final size:19
Alignment explanation
Indices: 14200--14237 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
14190 TATTATAATA
*
14200 TTTTAAAATTAATAATATT
1 TTTTAAAATAAATAATATT
*
14219 TTTTATAATAAATAATATT
1 TTTTAAAATAAATAATATT
14238 AATTATTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTTAAAATAAATAATATT
Found at i:14246 original size:22 final size:22
Alignment explanation
Indices: 14210--14264 Score: 55
Period size: 22 Copynumber: 2.6 Consensus size: 22
14200 TTTTAAAATT
14210 AATAATATT--TT-TTATAATA
1 AATAATATTAATTATTATAATA
* *
14229 AATAATATTAATTATTATATTC
1 AATAATATTAATTATTATAATA
14251 AATAAT-TATAATTA
1 AATAATAT-TAATTA
14265 ATCATTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
19 9 0.30
21 3 0.10
22 18 0.60
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (22 bp):
AATAATATTAATTATTATAATA
Found at i:17805 original size:138 final size:139
Alignment explanation
Indices: 17468--18215 Score: 1108
Period size: 138 Copynumber: 5.4 Consensus size: 139
17458 CGGGGACGCA
* * * * *
17468 CCTTTTATTATTTTATCAGAGAACATGTTATCATTGCCCTATTATGTCACTCGTGTCCCTCGAGG
1 CCTTCTATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGG
* * * * * * *
17533 GCACTATTCATGCCATTTCCTATTATGTTTGAGGGGATTTAGCAAATTGGTGAAGGCGCATTTCC
66 GCACTATTCATGTCAGTACCTATTATGTTTGAGGGGACTTAGCAAAGTGGTGAAAGCGCGTTTCC
* *
17598 GGGGGCGTG
131 GGGGGTGCG
* *
17607 CCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCTTATTATGTCACTCATGTCCCTCGGGG
1 CCTTCTATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGG
* * * * *
17672 GCACTATTCATATCAGTACCTATTATATTTGAGGGGACTTAGAAAAGTGGTGAAAGCGTGTTTTC
66 GCACTATTCATGTCAGTACCTATTATGTTTGAGGGGACTTAGCAAAGTGGTGAAAGCGCGTTTCC
17737 GGGGG-GCG
131 GGGGGTGCG
* *
17745 CATTCTATTATTTTGTCAGAGAATATGTCATCATTGCCCTATTATGTCACTCATGTCCCTCGGGG
1 CCTTCTATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGG
*
17810 GCACTATTCATGTCAGTACCTATTATGTTTGAGGGGACTTGGCAAAGTGGTGAAAGCGCGTTTCC
66 GCACTATTCATGTCAGTACCTATTATGTTTGAGGGGACTTAGCAAAGTGGTGAAAGCGCGTTTCC
17875 GGGGG-GCG
131 GGGGGTGCG
* * *
17883 CCTTCCATTATTTTGTCAGAGAATTTGTTATCATTGCCCTATTATGTCACTCATGTCCCTCAGGG
1 CCTTCTATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGG
* *
17948 GCACTATTTATGTCAGTACCTATTATGTTTGAGGGGACTTAGCAAAGTGGTGATAGCGCGTTTCC
66 GCACTATTCATGTCAGTACCTATTATGTTTGAGGGGACTTAGCAAAGTGGTGAAAGCGCGTTTCC
*
18013 GGGGGTGTG
131 GGGGGTGCG
* * * *
18022 TCTT-TCATTATTTTGTCAGAGAATATGTTATAATTGCCCTATTATGTGAGTCATGTCCC-CGGG
1 CCTTCT-ATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCGGG
* * * *
18085 GGAACTATTCATGTCCGTACCTATCATGTTTGAGGGGACTTAGCAAAGTGGTGAAAGCGCGTTTT
65 GGCACTATTCATGTCAGTACCTATTATGTTTGAGGGGACTTAGCAAAGTGGTGAAAGCGCGTTTC
18150 CGGGGGTGCG
130 CGGGGGTGCG
*
18160 CCTTCTATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTAATGT
1 CCTTCTATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGT
18216 TCTCGAAGAT
Statistics
Matches: 548, Mismatches: 58, Indels: 7
0.89 0.09 0.01
Matches are distributed among these distances:
138 377 0.69
139 171 0.31
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.35
Consensus pattern (139 bp):
CCTTCTATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGG
GCACTATTCATGTCAGTACCTATTATGTTTGAGGGGACTTAGCAAAGTGGTGAAAGCGCGTTTCC
GGGGGTGCG
Found at i:18034 original size:277 final size:276
Alignment explanation
Indices: 17469--18215 Score: 1120
Period size: 277 Copynumber: 2.7 Consensus size: 276
17459 GGGGACGCAC
* * * * *
17469 CTTTTATTATTTTATCAGAGAACATGTTATCATTGCCCTATTATGTCACTCGTGTCCCTCGAGGG
1 CTTTCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGG
* * * * * * *
17534 CACTATTCATGCCATTTCCTATTATGTTTGAGGGGATTTAGCAAATTGGTGAAGGCGCATTTCCG
66 CACTATTCATGTCAGTACCTATTATGTTTGAGGGGACTTAGCAAAGTGGTGAAAGCGCGTTTCCG
* *
17599 GGGGCGTGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCTTATTATGTCACTCATGTC
131 GGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTC
*
17664 CCTCGGGGGCACTATTCATATCAGTACCTATTATATTTGAGGGGACTTAGAAAAGTGGTGAAAGC
196 CCTCAGGGGCACTATTCATATCAGTACCTATTATATTTGAGGGGACTTAGAAAAGTGGTGAAAGC
* *
17729 GTGTTTTCGGGGGGCG
261 GCGTTTCCGGGGGGCG
* *
17745 CATTCTATTATTTTGTCAGAGAATATGTCATCATTGCCCTATTATGTCACTCATGTCCCTCGGGG
1 CTTTC-ATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGG
*
17810 GCACTATTCATGTCAGTACCTATTATGTTTGAGGGGACTTGGCAAAGTGGTGAAAGCGCGTTTCC
65 GCACTATTCATGTCAGTACCTATTATGTTTGAGGGGACTTAGCAAAGTGGTGAAAGCGCGTTTCC
*
17875 GGGGG-GCGCCTTCCATTATTTTGTCAGAGAATTTGTTATCATTGCCCTATTATGTCACTCATGT
130 GGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGT
* * * * *
17939 CCCTCAGGGGCACTATTTATGTCAGTACCTATTATGTTTGAGGGGACTTAGCAAAGTGGTGATAG
195 CCCTCAGGGGCACTATTCATATCAGTACCTATTATATTTGAGGGGACTTAGAAAAGTGGTGAAAG
*
18004 CGCGTTTCCGGGGGTGTG
260 CGCGTTTCCGGGGG-GCG
* * *
18022 TCTTTCATTATTTTGTCAGAGAATATGTTATAATTGCCCTATTATGTGAGTCATGTCCC-CGGGG
1 -CTTTCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGG
* * * *
18086 GAACTATTCATGTCCGTACCTATCATGTTTGAGGGGACTTAGCAAAGTGGTGAAAGCGCGTTTTC
65 GCACTATTCATGTCAGTACCTATTATGTTTGAGGGGACTTAGCAAAGTGGTGAAAGCGCGTTTCC
* * *
18151 GGGGGTGCGCCTTCTATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTAATGT
130 GGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGT
18216 TCTCGAAGAT
Statistics
Matches: 427, Mismatches: 40, Indels: 7
0.90 0.08 0.01
Matches are distributed among these distances:
276 200 0.47
277 223 0.52
278 4 0.01
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.35
Consensus pattern (276 bp):
CTTTCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGG
CACTATTCATGTCAGTACCTATTATGTTTGAGGGGACTTAGCAAAGTGGTGAAAGCGCGTTTCCG
GGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTC
CCTCAGGGGCACTATTCATATCAGTACCTATTATATTTGAGGGGACTTAGAAAAGTGGTGAAAGC
GCGTTTCCGGGGGGCG
Found at i:18687 original size:19 final size:19
Alignment explanation
Indices: 18646--18687 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
18636 GAATATAACT
*
18646 TTAAATTTTGAATACAATT
1 TTAAATTTTGAATACAATA
*
18665 TTAAATTTT-AATTCGAATA
1 TTAAATTTTGAATAC-AATA
18684 TTAA
1 TTAA
18688 GTTGAATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.48
Consensus pattern (19 bp):
TTAAATTTTGAATACAATA
Found at i:18708 original size:12 final size:12
Alignment explanation
Indices: 18668--18711 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
18658 TACAATTTTA
*
18668 AATTTTAATTCG
1 AATTTTAATTTG
* *
18680 AATATTAAGTTG
1 AATTTTAATTTG
18692 AATTTTAATTTG
1 AATTTTAATTTG
*
18704 TATTTTAA
1 AATTTTAA
18712 AAACATTTAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.36, C:0.02, G:0.09, T:0.52
Consensus pattern (12 bp):
AATTTTAATTTG
Found at i:20159 original size:21 final size:20
Alignment explanation
Indices: 20073--20230 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
20063 AAATGACCAA
**
20073 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
20092 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
20112 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
20132 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
20153 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
20174 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
20194 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
20215 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
20231 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:20259 original size:20 final size:20
Alignment explanation
Indices: 20197--20390 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
20187 CGATTTTCCA
* ** *
20197 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
20217 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
20237 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
20257 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
20277 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
20297 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
20317 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
20337 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
20357 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
20378 AAATCGCAACGCG
1 AAATCGCAACGCG
20391 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:20281 original size:60 final size:60
Alignment explanation
Indices: 20197--20390 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
20187 CGATTTTCCA
* ** * *
20197 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
20257 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
20317 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
20378 AAATCGCAACGCG
1 AAATCGCAACGCG
20391 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:20810 original size:33 final size:33
Alignment explanation
Indices: 20771--20841 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
20761 TTCACTTAGA
* *
20771 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
* *
20804 TTTCATTTCGCGTTGCTATTCTCTCGTTCCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
20837 TTTCA
1 TTTCA
20842 AGTTAGTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
Found at i:20965 original size:20 final size:20
Alignment explanation
Indices: 20921--20995 Score: 89
Period size: 20 Copynumber: 3.8 Consensus size: 20
20911 TGCAGAAGAG
* *
20921 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-GAATGACAA
**
20942 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAGAATGACAA
*
20962 TCGCAACGCGAG-ATGACAA
1 TCGCAACGAGAGAATGACAA
20981 TCGCAACGAGAGAAT
1 TCGCAACGAGAGAAT
20996 CGCAACGCGA
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
19 16 0.36
20 18 0.40
21 11 0.24
ACGTcount: A:0.41, C:0.20, G:0.25, T:0.13
Consensus pattern (20 bp):
TCGCAACGAGAGAATGACAA
Found at i:20984 original size:19 final size:19
Alignment explanation
Indices: 20935--21026 Score: 77
Period size: 19 Copynumber: 5.1 Consensus size: 19
20925 AACGAGATAA
*
20935 ATGAAAATCGCAACGAGAG
1 ATGAAAATCGCAACGCGAG
***
20954 AATGACTGTCGCAACGCGAG
1 -ATGAAAATCGCAACGCGAG
*
20974 ATGACAATCGCAA--CGAG
1 ATGAAAATCGCAACGCGAG
*
20991 A-G--AATCGCAACGCGAA
1 ATGAAAATCGCAACGCGAG
*
21007 ATGAAAATCGCAACGAGAG
1 ATGAAAATCGCAACGCGAG
21026 A
1 A
21027 ATCGCAACGC
Statistics
Matches: 58, Mismatches: 9, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
14 8 0.14
16 5 0.09
17 6 0.10
19 24 0.41
20 15 0.26
ACGTcount: A:0.42, C:0.21, G:0.26, T:0.11
Consensus pattern (19 bp):
ATGAAAATCGCAACGCGAG
Found at i:20998 original size:14 final size:14
Alignment explanation
Indices: 20979--21035 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
20969 GCGAGATGAC
20979 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
20993 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
21012 AATCGCAACGAGAG
1 AATCGCAACGAGAG
21026 AATCGCAACG
1 AATCGCAACG
21036 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:21004 original size:33 final size:33
Alignment explanation
Indices: 20933--21051 Score: 148
Period size: 33 Copynumber: 3.4 Consensus size: 33
20923 GCAACGAGAT
20933 AAATGAAAATCGCAACGAGAGAATGACTGTCGCAACGCG
1 AAATGAAAATCGCAACGAGAG-A--A---TCGCAACGCG
* *
20972 AGATGACAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
21005 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
**
21038 AAACCAAAATCGCA
1 AAATGAAAATCGCA
21052 TTGCGATTTT
Statistics
Matches: 74, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
33 53 0.72
36 1 0.01
38 1 0.01
39 19 0.26
ACGTcount: A:0.44, C:0.23, G:0.24, T:0.10
Consensus pattern (33 bp):
AAATGAAAATCGCAACGAGAGAATCGCAACGCG
Found at i:21069 original size:19 final size:19
Alignment explanation
Indices: 21047--21144 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
21037 GAAACCAAAA
*
21047 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
21066 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
21080 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
21099 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
21113 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
21132 TCGCGTTGCGATT
1 TCGCGTTGCGATT
21145 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:21088 original size:14 final size:14
Alignment explanation
Indices: 21069--21158 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
21059 TTTCATTTCG
21069 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
21083 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
21102 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
21116 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
21133 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
21149 CGTTGCGATT
1 CGTTGCGATT
21159 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:21094 original size:33 final size:33
Alignment explanation
Indices: 21052--21166 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
21042 CAAAATCGCA
21052 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
21085 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
21118 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
21151 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
21167 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:23279 original size:92 final size:93
Alignment explanation
Indices: 22860--23424 Score: 1107
Period size: 93 Copynumber: 6.1 Consensus size: 93
22850 TAGATTGCTT
*
22860 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
22925 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
22953 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
23018 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
23046 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
23111 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
23139 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
23204 TTTGTCTTTG-TTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
23231 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
23296 TTTGTC-TTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
23323 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
23388 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
23416 AGTAAATTT
1 AGTAAATTT
23425 ATCCATTCAA
Statistics
Matches: 469, Mismatches: 1, Indels: 4
0.99 0.00 0.01
Matches are distributed among these distances:
91 3 0.01
92 176 0.38
93 290 0.62
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:23508 original size:19 final size:19
Alignment explanation
Indices: 23468--23596 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
23458 TAGTTTACTT
* *
23468 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
23488 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
23507 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
23526 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
23540 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
23559 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
23573 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
23592 TCGCA
1 TCGCA
23597 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:23547 original size:33 final size:32
Alignment explanation
Indices: 23504--23596 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
23494 CGCGAAACCA
**
23504 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
23536 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
23569 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
23597 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:23594 original size:52 final size:52
Alignment explanation
Indices: 23468--23596 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
23458 TAGTTTACTT
**
23468 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
23520 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
23573 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
23597 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:23614 original size:19 final size:18
Alignment explanation
Indices: 23592--23709 Score: 108
Period size: 19 Copynumber: 6.8 Consensus size: 18
23582 GAAACCAAAA
*
23592 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTC-TT
23611 TCGCGTTGCGA--TTCTT
1 TCGCGTTGCGATTTTCTT
*
23627 T--CGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTT-CTT
*
23644 TCGCGTTGCGA--TTCTG
1 TCGCGTTGCGATTTTCTT
23660 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTC-TT
**
23677 TCGCGTTGCGATTTGGTT
1 TCGCGTTGCGATTTTCTT
23695 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
23710 AAGTTTCGTG
Statistics
Matches: 81, Mismatches: 8, Indels: 21
0.74 0.07 0.19
Matches are distributed among these distances:
14 16 0.20
16 10 0.12
17 10 0.12
18 16 0.20
19 29 0.36
ACGTcount: A:0.08, C:0.19, G:0.25, T:0.47
Consensus pattern (18 bp):
TCGCGTTGCGATTTTCTT
Found at i:23633 original size:14 final size:14
Alignment explanation
Indices: 23614--23670 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
23604 TTTCATTTCG
23614 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
*
23628 CGTTGCGATTTTGGTTT
1 CGTTGCGA--TT-CTTT
*
23645 CGCGTTGCGATTCTGT
1 --CGTTGCGATTCTTT
23661 CGTTGCGATT
1 CGTTGCGATT
23671 TTCATTTCGC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 18 0.51
16 4 0.11
17 5 0.14
19 8 0.23
ACGTcount: A:0.07, C:0.19, G:0.28, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:23639 original size:33 final size:33
Alignment explanation
Indices: 23597--23725 Score: 159
Period size: 33 Copynumber: 3.8 Consensus size: 33
23587 CAAAATCGCA
23597 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
** *
23630 TTGCGATTTTGGTTTCGCGTTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
*
23663 TTGCGATTTTCATTTCGCGTTGCGATTTGGTTTCGCG
1 TTGCGATTTTCATTTCGCGTTGCGA-TT-CTTT--CG
* *
23700 TTGCGATTTTAAGTTTCGTGTTGCGA
1 TTGCGATTTTCA-TTTCGCGTTGCGA
23726 AAGTAAACTA
Statistics
Matches: 82, Mismatches: 9, Indels: 5
0.85 0.09 0.05
Matches are distributed among these distances:
33 53 0.65
34 2 0.02
35 2 0.02
37 13 0.16
38 12 0.15
ACGTcount: A:0.09, C:0.18, G:0.26, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
Found at i:25671 original size:14 final size:14
Alignment explanation
Indices: 25652--25687 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
25642 ATTGTTTAAT
25652 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
25666 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
25680 TGATTTGT
1 TGATTTGT
25688 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:25817 original size:19 final size:19
Alignment explanation
Indices: 25793--25892 Score: 129
Period size: 19 Copynumber: 5.5 Consensus size: 19
25783 AAAATTGACT
25793 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
25812 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
25831 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
25845 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
25864 ATCGCAATGCATAAATGAAA
1 ATCGCAATGC-GAAATGAAA
25884 ATCGCAATG
1 ATCGCAATG
25893 GGAGAATCGC
Statistics
Matches: 71, Mismatches: 4, Indels: 11
0.83 0.05 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 38 0.54
20 17 0.24
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:25903 original size:53 final size:52
Alignment explanation
Indices: 25793--25909 Score: 189
Period size: 53 Copynumber: 2.2 Consensus size: 52
25783 AAAATTGACT
25793 ATCGCAATGCGAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAGA
* * * *
25845 ATCGCAATGCGAAATGAAAATCGCAATGCATAAATGAAAATCGCAATGGGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGC-GAAATGAAAATCGCAACGAGAGA
25898 ATCGCAATGCGA
1 ATCGCAATGCGA
25910 TTTTAATTTC
Statistics
Matches: 60, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
52 28 0.47
53 32 0.53
ACGTcount: A:0.44, C:0.18, G:0.23, T:0.15
Consensus pattern (52 bp):
ATCGCAATGCGAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:25927 original size:19 final size:19
Alignment explanation
Indices: 25899--26031 Score: 142
Period size: 19 Copynumber: 7.5 Consensus size: 19
25889 AATGGGAGAA
* *
25899 TCGCAATGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
*
25918 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
*
25934 TCG--TTGCGATTCTCATT
1 TCGCATTGCGATTTTCATT
25951 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
25970 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
25989 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
26005 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
26022 TCGGCATTGC
1 TC-GCATTGC
26032 AAAATGTAAT
Statistics
Matches: 95, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 12 0.13
16 13 0.14
17 12 0.13
18 1 0.01
19 53 0.56
20 4 0.04
ACGTcount: A:0.15, C:0.23, G:0.18, T:0.44
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:25980 original size:71 final size:72
Alignment explanation
Indices: 25899--26031 Score: 232
Period size: 71 Copynumber: 1.9 Consensus size: 72
25889 AATGGGAGAA
25899 TCGCAATGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTCTCATTTC-GCATTGCGAT
1 TCGCAATGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTCTCATTTCGGCATTGCGAT
25963 TTTCATT
66 TTTCATT
* * *
25970 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGGCATTGC
1 TCGCAATGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTCTCATTTCGGCATTGC
26032 AAAATGTAAT
Statistics
Matches: 58, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
71 51 0.88
72 7 0.12
ACGTcount: A:0.15, C:0.23, G:0.18, T:0.44
Consensus pattern (72 bp):
TCGCAATGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTCTCATTTCGGCATTGCGAT
TTTCATT
Found at i:26012 original size:52 final size:49
Alignment explanation
Indices: 25905--26031 Score: 141
Period size: 52 Copynumber: 2.4 Consensus size: 49
25895 AGAATCGCAA
*
25905 TGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTCTCATTTCGCAT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTCTC--TTCG-AT
*
25957 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTC-TCG-T
1 TGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTCTCTTCGAT
26009 TGCGATTTTCATTTCGGCATTGC
1 TGCGATTTTCATTTC-GCATTGC
26032 AAAATGTAAT
Statistics
Matches: 67, Mismatches: 2, Indels: 11
0.84 0.03 0.14
Matches are distributed among these distances:
52 39 0.58
53 7 0.10
54 6 0.09
55 4 0.06
57 11 0.16
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (49 bp):
TGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTCTCTTCGAT
Found at i:26116 original size:19 final size:19
Alignment explanation
Indices: 26092--26189 Score: 134
Period size: 19 Copynumber: 5.4 Consensus size: 19
26082 AAAATTGACT
*
26092 ATCGCAATGCAAAATGAAA
1 ATCGCAATGCGAAATGAAA
26111 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
26130 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
26144 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
26163 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
26183 ATCGCAA
1 ATCGCAA
26190 CGAGAGAATC
Statistics
Matches: 70, Mismatches: 3, Indels: 11
0.83 0.04 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 38 0.54
20 16 0.23
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:26221 original size:53 final size:53
Alignment explanation
Indices: 26092--26208 Score: 218
Period size: 53 Copynumber: 2.2 Consensus size: 53
26082 AAAATTGACT
*
26092 ATCGCAATGCAAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
26144 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
26197 ATCGCAATGCGA
1 ATCGCAATGCGA
26209 TTTTCATTTC
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 28 0.44
53 35 0.56
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:28541 original size:12 final size:12
Alignment explanation
Indices: 28524--28548 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28514 TCTTCGGGGA
28524 CTTTTTCTTCTT
1 CTTTTTCTTCTT
28536 CTTTTTCTTCTT
1 CTTTTTCTTCTT
28548 C
1 C
28549 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:29480 original size:20 final size:20
Alignment explanation
Indices: 29452--29701 Score: 232
Period size: 20 Copynumber: 12.5 Consensus size: 20
29442 AAATTTCAGT
* * *
29452 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
29472 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
29492 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
* **
29512 TTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
29532 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
*
29552 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* * *
29572 ATTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* * ** *
29592 ATTGTGATTTACCCATACGC
1 GTTGCGATTTACGGATTCGC
* *
29612 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
29632 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
29652 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
29672 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
29692 GTTGCGATTT
1 GTTGCGATTT
29702 TGGAAAATCG
Statistics
Matches: 196, Mismatches: 32, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
20 195 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:29718 original size:21 final size:21
Alignment explanation
Indices: 29688--29770 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
29678 ATTTTCATAT
*
29688 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
29709 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
29730 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
29751 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
29771 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:29761 original size:42 final size:43
Alignment explanation
Indices: 29668--29766 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
29658 ATTTATGTGT
* *
29668 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
29709 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
29751 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
29767 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:31043 original size:11 final size:11
Alignment explanation
Indices: 30992--31043 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
30982 AATTAGCACC
30992 AATAATAATTA
1 AATAATAATTA
*
31003 ATTAATTAATTTA
1 AATAA-TAA-TTA
*
31016 AATAAATAAATA
1 AAT-AATAATTA
31028 AATAATAATTA
1 AATAATAATTA
*
31039 TATAA
1 AATAA
31044 ATATTATTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
11 15 0.45
12 8 0.24
13 8 0.24
14 2 0.06
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
AATAATAATTA
Found at i:31043 original size:15 final size:15
Alignment explanation
Indices: 31025--31084 Score: 50
Period size: 15 Copynumber: 3.8 Consensus size: 15
31015 AAATAAATAA
31025 ATAAATAATAATTAT
1 ATAAATAATAATTAT
* *
31040 ATAAATATTATTTTAAT
1 ATAAATAATA-ATT-AT
*
31057 AATAAAATAATATTTAT
1 -AT-AAATAATAATTAT
31074 ATAAAT-ATAAT
1 ATAAATAATAAT
31085 AATAAAAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
14 4 0.11
15 13 0.35
16 4 0.11
17 4 0.11
18 5 0.14
19 7 0.19
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
ATAAATAATAATTAT
Found at i:31383 original size:60 final size:61
Alignment explanation
Indices: 31308--31451 Score: 177
Period size: 60 Copynumber: 2.4 Consensus size: 61
31298 TTACTGGAAG
* * * *
31308 GCGCGTCCCCGGGGATGCGTCTTACCCCCGTGGCATCCGACTCAGC-AAAACCC-CGTGAAA
1 GCGCGTCCCCAGGGATGCGCCTTACCCCCGTGGCATCCCACTCAGCTAAAACCCAGGT-AAA
* * *
31368 GCGCGTCCCCAGGGATGCACCTTACCCGCGTGGCATCCCAGTCAGCTAAAACCCAGGTAAA
1 GCGCGTCCCCAGGGATGCGCCTTACCCCCGTGGCATCCCACTCAGCTAAAACCCAGGTAAA
*
31429 -CTGTGTCCCCAGGGATGCGCCTT
1 GC-GCGTCCCCAGGGATGCGCCTT
31452 TGTGCCACCT
Statistics
Matches: 72, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
60 41 0.57
61 29 0.40
62 2 0.03
ACGTcount: A:0.20, C:0.37, G:0.26, T:0.17
Consensus pattern (61 bp):
GCGCGTCCCCAGGGATGCGCCTTACCCCCGTGGCATCCCACTCAGCTAAAACCCAGGTAAA
Found at i:40739 original size:24 final size:20
Alignment explanation
Indices: 40690--40748 Score: 73
Period size: 20 Copynumber: 2.8 Consensus size: 20
40680 TTCCCATTGA
*
40690 AGTGCATCGGTGCATTCTAC
1 AGTGCATCGATGCATTCTAC
40710 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
40733 AGGTGCATCGATGCAT
1 A-GTGCATCGATGCAT
40749 GGTTGCACTA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
20 16 0.47
22 1 0.03
23 3 0.09
24 14 0.41
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.31
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:48687 original size:2 final size:2
Alignment explanation
Indices: 48680--48727 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
48670 TTACACAATC
48680 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
48722 AT AT AT
1 AT AT AT
48728 GCTATCAATA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:48829 original size:20 final size:22
Alignment explanation
Indices: 48804--48861 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
48794 TTCCCATTGA
48804 AGTGCATCGATGCATTC-T-AC
1 AGTGCATCGATGCATTCTTAAC
48824 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC-TTAAC
48847 AGGTGCATCGATGCA
1 A-GTGCATCGATGCA
48862 CTACCATGCA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 17 0.50
22 1 0.03
23 3 0.09
24 13 0.38
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.29
Consensus pattern (22 bp):
AGTGCATCGATGCATTCTTAAC
Found at i:52716 original size:2 final size:2
Alignment explanation
Indices: 52709--52752 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
52699 CTACACAATC
52709 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
52751 AT
1 AT
52753 GCTATCAATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:56936 original size:24 final size:20
Alignment explanation
Indices: 56887--56944 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
56877 TTCCCATTGA
*
56887 AGTGCATCGGTGCATTCTAC
1 AGTGCATCGATGCATTCTAC
56907 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
56930 AGGTGCATCGATGCA
1 A-GTGCATCGATGCA
56945 CTACCATGCA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 16 0.48
22 1 0.03
23 3 0.09
24 13 0.39
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.29
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:63381 original size:31 final size:31
Alignment explanation
Indices: 63343--63413 Score: 115
Period size: 31 Copynumber: 2.3 Consensus size: 31
63333 GTGGACTTGC
63343 CACAAATTTATGACATATTCACCTATTCTGT
1 CACAAATTTATGACATATTCACCTATTCTGT
* * *
63374 CACAAATTTCTGACATGTTCACTTATTCTGT
1 CACAAATTTATGACATATTCACCTATTCTGT
63405 CACAAATTT
1 CACAAATTT
63414 GTGATGTCAG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.31, C:0.23, G:0.07, T:0.39
Consensus pattern (31 bp):
CACAAATTTATGACATATTCACCTATTCTGT
Found at i:63427 original size:16 final size:16
Alignment explanation
Indices: 63402--63435 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
63392 TCACTTATTC
63402 TGTCACAAATTTGTGA
1 TGTCACAAATTTGTGA
*
63418 TGTCAGAAATTTGTGA
1 TGTCACAAATTTGTGA
63434 TG
1 TG
63436 AATCCACATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (16 bp):
TGTCACAAATTTGTGA
Found at i:63548 original size:31 final size:31
Alignment explanation
Indices: 63513--63577 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
63503 TTGTGGACCC
*
63513 GTCACAAATTTCTAACATATCCACCTATTCT
1 GTCACAAATTTCTAACATATCCACATATTCT
* * * *
63544 GTCACAAATTTGTGACATGTCCACATGTTCT
1 GTCACAAATTTCTAACATATCCACATATTCT
63575 GTC
1 GTC
63578 GTAATTTTGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.28, C:0.26, G:0.11, T:0.35
Consensus pattern (31 bp):
GTCACAAATTTCTAACATATCCACATATTCT
Done.