Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014429.1 Corchorus capsularis cultivar CVL-1 contig14450, 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: 148697
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:854 original size:22 final size:23
Alignment explanation
Indices: 812--856 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
802 TGAAACAAGA
812 CAAACGCTCTCACAAAGGAGTCC
1 CAAACGCTCTCACAAAGGAGTCC
*
835 CAAATGCTCTCAC-AAGGAGTCC
1 CAAACGCTCTCACAAAGGAGTCC
857 TGATTATGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.33, C:0.33, G:0.18, T:0.16
Consensus pattern (23 bp):
CAAACGCTCTCACAAAGGAGTCC
Found at i:2124 original size:182 final size:177
Alignment explanation
Indices: 1765--2125 Score: 551
Period size: 182 Copynumber: 2.0 Consensus size: 177
1755 TCCATAAACA
* *
1765 AATCATTTTTTTGTTGAATTATTTATTAAATGATCCTCGTACTTTTATAATTTATGCTATTTAAT
1 AATCATTTTTTTGTTGAATTATTTATTAAATGATCCTCATACTTTTATAATTTATACTATTTAAT
* * * *
1830 TCTTACAATTATATGTTGGACGATTGAATGTTTCGGCTTTAATTGTTTTTTTTTTCTATTTGGCC
66 ACTTACAATTATAGGTTGGACAATTGAATGTTTCGGCTTTAATTGTTTTTTTTTTCTATTTGACC
* * *
1895 AATCAAGGTGATTCAGGTGTCTATTTACAGGTAATTCCATGGTCTAC
131 AATCAAGGTGATTCAAGTGTCTATTTAAAGGTAATTCCATAGTCTAC
*
1942 AATCATTTTTTTTGTTGGATTATTTATTAAATGATCCTCATACTTTTATAATTTATACTATTTAA
1 AATCA-TTTTTTTGTTGAATTATTTATTAAATGATCCTCATACTTTTATAATTTATACTATTTAA
* * *
2007 TCACTTACAATTATGGGTTGGATAATTGAATGTTTCGGCTTTAATTCTTTTATTTTTTTTCTATT
65 T-ACTTACAATTATAGGTTGGACAATTGAATGTTTCGGCTTTAA-T-TGTT-TTTTTTTTCTATT
*
2072 TGACCGATCAAGGTGATTCAAGTGTCTATTTAAAGGTAATTCCATAGTCTAC
126 TGACCAATCAAGGTGATTCAAGTGTCTATTTAAAGGTAATTCCATAGTCTAC
2124 AA
1 AA
2126 CTTTCATGAA
Statistics
Matches: 165, Mismatches: 14, Indels: 5
0.90 0.08 0.03
Matches are distributed among these distances:
177 5 0.03
178 57 0.35
179 37 0.22
180 1 0.01
181 3 0.02
182 62 0.38
ACGTcount: A:0.27, C:0.12, G:0.14, T:0.48
Consensus pattern (177 bp):
AATCATTTTTTTGTTGAATTATTTATTAAATGATCCTCATACTTTTATAATTTATACTATTTAAT
ACTTACAATTATAGGTTGGACAATTGAATGTTTCGGCTTTAATTGTTTTTTTTTTCTATTTGACC
AATCAAGGTGATTCAAGTGTCTATTTAAAGGTAATTCCATAGTCTAC
Found at i:4273 original size:19 final size:19
Alignment explanation
Indices: 4237--4273 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
4227 AAAAATATGA
**
4237 GTAAAAAATAATTTAAAAT
1 GTAAAAAATAATAAAAAAT
4256 GTAAAAAATAATAAAAAA
1 GTAAAAAATAATAAAAAA
4274 AAACCACATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.24
Consensus pattern (19 bp):
GTAAAAAATAATAAAAAAT
Found at i:4959 original size:3 final size:3
Alignment explanation
Indices: 4951--4978 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
4941 TTTAGATATA
4951 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
4979 CATTTTTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:5074 original size:27 final size:27
Alignment explanation
Indices: 5056--5109 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
5046 ATTATATATG
*
5056 AAGAAAAATTCTCTATAATTTCCACTC
1 AAGAAAAATTCTCTATAATTTACACTC
*
5083 AAGAAAAATTCTCTATAATTTCCACTC
1 AAGAAAAATTCTCTATAATTTACACTC
5110 TTCCATCATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.41, C:0.22, G:0.04, T:0.33
Consensus pattern (27 bp):
AAGAAAAATTCTCTATAATTTACACTC
Found at i:5437 original size:8 final size:7
Alignment explanation
Indices: 5409--5435 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
5399 ATCCTTGTTA
5409 AAAAAAG
1 AAAAAAG
5416 AAAAAAG
1 AAAAAAG
5423 AAAAAAG
1 AAAAAAG
5430 AAAAAA
1 AAAAAA
5436 AGGATTTCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:12604 original size:19 final size:19
Alignment explanation
Indices: 12576--12613 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
12566 CGGATTTTTT
*
12576 TATAACAAGTATTTTCGGA
1 TATAAAAAGTATTTTCGGA
12595 TATAAAAAGTATTTTCGGA
1 TATAAAAAGTATTTTCGGA
12614 CCAAGCATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.39, C:0.08, G:0.16, T:0.37
Consensus pattern (19 bp):
TATAAAAAGTATTTTCGGA
Found at i:17619 original size:15 final size:15
Alignment explanation
Indices: 17599--17629 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
17589 AGCCATGTGG
17599 GGACTTGGTTGCCAT
1 GGACTTGGTTGCCAT
17614 GGACTTGGTTGCCAT
1 GGACTTGGTTGCCAT
17629 G
1 G
17630 AGCCATGTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.13, C:0.19, G:0.35, T:0.32
Consensus pattern (15 bp):
GGACTTGGTTGCCAT
Found at i:17671 original size:24 final size:25
Alignment explanation
Indices: 17614--17678 Score: 96
Period size: 26 Copynumber: 2.6 Consensus size: 25
17604 TGGTTGCCAT
*
17614 GGACTTGGTTGCCATGAGCCATGTGG
1 GGACTTGGTTGCCATAAGCCA-GTGG
*
17640 GGATTTGGTTGCCATAAGCCA-TGG
1 GGACTTGGTTGCCATAAGCCAGTGG
17664 GGACTTGGTTGCCAT
1 GGACTTGGTTGCCAT
17679 GGACTTGGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
24 17 0.47
26 19 0.53
ACGTcount: A:0.17, C:0.18, G:0.35, T:0.29
Consensus pattern (25 bp):
GGACTTGGTTGCCATAAGCCAGTGG
Found at i:17674 original size:65 final size:65
Alignment explanation
Indices: 17581--17718 Score: 242
Period size: 65 Copynumber: 2.1 Consensus size: 65
17571 GGTTGCCAAC
*
17581 TTGCCATGAGCCATGTGGGGACTTGGTTGCCATGGACTTGGTTGCCATGAGCCATGTGGGGATTT
1 TTGCCATAAGCCA-GTGGGGACTTGGTTGCCATGGACTTGGTTGCCATGAGCCATGT-GGGATTT
17646 GG
64 GG
17648 TTGCCATAAGCCA-TGGGGACTTGGTTGCCATGGACTTGGTTGCCATGAGCCATGTGGGATTTGG
1 TTGCCATAAGCCAGTGGGGACTTGGTTGCCATGGACTTGGTTGCCATGAGCCATGTGGGATTTGG
17712 TTGCCAT
1 TTGCCAT
17719 GGACTTGGTT
Statistics
Matches: 70, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
64 16 0.23
65 42 0.60
67 12 0.17
ACGTcount: A:0.16, C:0.19, G:0.35, T:0.30
Consensus pattern (65 bp):
TTGCCATAAGCCAGTGGGGACTTGGTTGCCATGGACTTGGTTGCCATGAGCCATGTGGGATTTGG
Found at i:17679 original size:17 final size:16
Alignment explanation
Indices: 17657--17694 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
17647 GTTGCCATAA
17657 GCCATGGGGACTTGGTT
1 GCCAT-GGGACTTGGTT
17674 GCCAT-GGACTTGGTT
1 GCCATGGGACTTGGTT
17689 GCCATG
1 GCCATG
17695 AGCCATGTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 15 0.75
17 5 0.25
ACGTcount: A:0.13, C:0.21, G:0.37, T:0.29
Consensus pattern (16 bp):
GCCATGGGACTTGGTT
Found at i:17684 original size:15 final size:15
Alignment explanation
Indices: 17664--17694 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
17654 TAAGCCATGG
17664 GGACTTGGTTGCCAT
1 GGACTTGGTTGCCAT
17679 GGACTTGGTTGCCAT
1 GGACTTGGTTGCCAT
17694 G
1 G
17695 AGCCATGTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.13, C:0.19, G:0.35, T:0.32
Consensus pattern (15 bp):
GGACTTGGTTGCCAT
Found at i:17693 original size:39 final size:40
Alignment explanation
Indices: 17644--17733 Score: 146
Period size: 40 Copynumber: 2.3 Consensus size: 40
17634 ATGTGGGGAT
17644 TTGGTTGCCATAAGCCATG-GGGACTTGGTTGCCATGGAC
1 TTGGTTGCCATAAGCCATGTGGGACTTGGTTGCCATGGAC
* *
17683 TTGGTTGCCATGAGCCATGTGGGATTTGGTTGCCATGGAC
1 TTGGTTGCCATAAGCCATGTGGGACTTGGTTGCCATGGAC
*
17723 TTGGTTACCAT
1 TTGGTTGCCAT
17734 TGGTTGCCAT
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
39 18 0.38
40 29 0.62
ACGTcount: A:0.17, C:0.19, G:0.32, T:0.32
Consensus pattern (40 bp):
TTGGTTGCCATAAGCCATGTGGGACTTGGTTGCCATGGAC
Found at i:17713 original size:25 final size:25
Alignment explanation
Indices: 17683--17794 Score: 115
Period size: 25 Copynumber: 4.5 Consensus size: 25
17673 TGCCATGGAC
17683 TTGGTTGCCATGAGCCATGTGGGAT
1 TTGGTTGCCATGAGCCATGTGGGAT
* * *
17708 TTGGTTGCCATG-GAC-T-TGGTTACCA
1 TTGGTTGCCATGAGCCATGTGG-GA--T
*
17733 TTGGTTGCCATGAGCTATGTGGGAT
1 TTGGTTGCCATGAGCCATGTGGGAT
* *
17758 TTGGTTTCCATGAGCCATG-GGGAC
1 TTGGTTGCCATGAGCCATGTGGGAT
17782 TTGGTTGCCATGA
1 TTGGTTGCCATGA
17795 TACGACACAT
Statistics
Matches: 70, Mismatches: 11, Indels: 13
0.74 0.12 0.14
Matches are distributed among these distances:
22 3 0.04
23 2 0.03
24 18 0.26
25 41 0.59
26 1 0.01
27 2 0.03
28 3 0.04
ACGTcount: A:0.16, C:0.17, G:0.33, T:0.34
Consensus pattern (25 bp):
TTGGTTGCCATGAGCCATGTGGGAT
Found at i:18573 original size:12 final size:13
Alignment explanation
Indices: 18548--18576 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
18538 AGTACAGTCC
18548 AAAACATAAAACT
1 AAAACATAAAACT
18561 AAAACAT-AAACT
1 AAAACATAAAACT
18573 AAAA
1 AAAA
18577 TGCAAATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.72, C:0.14, G:0.00, T:0.14
Consensus pattern (13 bp):
AAAACATAAAACT
Found at i:19993 original size:31 final size:31
Alignment explanation
Indices: 19858--19992 Score: 180
Period size: 31 Copynumber: 4.4 Consensus size: 31
19848 GTATCCGACG
*
19858 TGGCATGCCATGTGTACCAAAAAGTGACACA
1 TGGCATGCCACGTGTACCAAAAAGTGACACA
** *
19889 TTTCACGCCACGTGTACCAAAAAGTGACACA
1 TGGCATGCCACGTGTACCAAAAAGTGACACA
** * *
19920 TTTCACGCCACGTGTACCAAAAAATGACACA
1 TGGCATGCCACGTGTACCAAAAAGTGACACA
* *
19951 TGGCATGCCACATGTACCAGAAAGTGACACA
1 TGGCATGCCACGTGTACCAAAAAGTGACACA
19982 TGGCATGCCAC
1 TGGCATGCCAC
19993 AAACACAAAA
Statistics
Matches: 93, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 93 1.00
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.19
Consensus pattern (31 bp):
TGGCATGCCACGTGTACCAAAAAGTGACACA
Found at i:24673 original size:22 final size:22
Alignment explanation
Indices: 24645--24689 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
24635 GAAAACCCAG
*
24645 TGGGACAAAATTGAACAGAAGA
1 TGGGACAAAATCGAACAGAAGA
24667 TGGGACAAAATCGAACAGAAGA
1 TGGGACAAAATCGAACAGAAGA
24689 T
1 T
24690 CGAAGTTTCG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.49, C:0.11, G:0.27, T:0.13
Consensus pattern (22 bp):
TGGGACAAAATCGAACAGAAGA
Found at i:24951 original size:47 final size:46
Alignment explanation
Indices: 24784--24949 Score: 251
Period size: 46 Copynumber: 3.6 Consensus size: 46
24774 CTTGTGTAAT
24784 AACTTCTGGTGTCAATTAAATTTACTAAAGAAAATTTTGATTTGAC
1 AACTTCTGGTGTCAATTAAATTTACTAAAGAAAATTTTGATTTGAC
* * *
24830 AAATTTTGGTGTCAATTAAATTTATTAAAGAAAATTTTGATTTGAC
1 AACTTCTGGTGTCAATTAAATTTACTAAAGAAAATTTTGATTTGAC
* * * * *
24876 AACTTCTAGTGTAAATTAAATTTACTAGAATAAAATTTTAATTTTAC
1 AACTTCTGGTGTCAATTAAATTTACTA-AAGAAAATTTTGATTTGAC
24923 AACTTCTGGTGTCAATTAAATTTACTA
1 AACTTCTGGTGTCAATTAAATTTACTA
24950 GAGCTCTCGT
Statistics
Matches: 106, Mismatches: 13, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
46 65 0.61
47 41 0.39
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.42
Consensus pattern (46 bp):
AACTTCTGGTGTCAATTAAATTTACTAAAGAAAATTTTGATTTGAC
Found at i:25772 original size:2 final size:2
Alignment explanation
Indices: 25767--25800 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
25757 TGTGTGTGTG
25767 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
25801 ATAAGGTGGA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:36017 original size:62 final size:62
Alignment explanation
Indices: 35918--36069 Score: 223
Period size: 62 Copynumber: 2.5 Consensus size: 62
35908 ATATTCATAC
* * *
35918 GAAATTATGATAACCTTCCTATTAAATTATGAGAATTACACTATTCTTGATAACGTCCTTAT
1 GAAATTTTGATAACCTTCATATGAAATTATGAGAATTACACTATTCTTGATAACGTCCTTAT
* * * * *
35980 GAAATTTTGATAACCTTCATATGCAATTATGATAATTACACTATTTTTTATGACGTCCTTAT
1 GAAATTTTGATAACCTTCATATGAAATTATGAGAATTACACTATTCTTGATAACGTCCTTAT
*
36042 GAAATTTTAATAACCTTCATATGAAATT
1 GAAATTTTGATAACCTTCATATGAAATT
36070 TCAATAATGA
Statistics
Matches: 80, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
62 80 1.00
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (62 bp):
GAAATTTTGATAACCTTCATATGAAATTATGAGAATTACACTATTCTTGATAACGTCCTTAT
Found at i:36120 original size:20 final size:21
Alignment explanation
Indices: 36095--36141 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
36085 TGGAATTTCG
* *
36095 AACCTTTTTAT-AATTTTTTT
1 AACCTTCTTATAAATTTTGTT
36115 AACCTTCTTATGAAATTTTGTT
1 AACCTTCTTAT-AAATTTTGTT
36137 AACCT
1 AACCT
36142 CCCTAAGGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 10 0.43
22 13 0.57
ACGTcount: A:0.28, C:0.15, G:0.04, T:0.53
Consensus pattern (21 bp):
AACCTTCTTATAAATTTTGTT
Found at i:36352 original size:23 final size:23
Alignment explanation
Indices: 36321--36405 Score: 102
Period size: 23 Copynumber: 3.7 Consensus size: 23
36311 GATAATCTCG
*
36321 CTATGAAATTTTGATAAACCTTC
1 CTATAAAATTTTGATAAACCTTC
* *
36344 CTATAAAATTTTGATAAATCTCC
1 CTATAAAATTTTGATAAACCTTC
36367 CTATAAAATTTTGAT-AACC-TC
1 CTATAAAATTTTGATAAACCTTC
* *
36388 CTTATGAAATCTTGATAA
1 C-TATAAAATTTTGATAA
36406 CTACAAATTT
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
21 2 0.04
22 15 0.28
23 36 0.68
ACGTcount: A:0.38, C:0.16, G:0.07, T:0.39
Consensus pattern (23 bp):
CTATAAAATTTTGATAAACCTTC
Found at i:36485 original size:82 final size:84
Alignment explanation
Indices: 36326--36488 Score: 204
Period size: 82 Copynumber: 2.0 Consensus size: 84
36316 TCTCGCTATG
* * * *
36326 AAATTTTGATAAACCTTCCTATAAAATTTTGATAAATCTCCCTATAAAATTTTGATAACCTCCTT
1 AAATTTTGATAAACCTCCCTATAAAATTTTGATAAACCTCACTATAAAATTTTGATAACCTCCCT
36391 ATGAAATCTTGATAACTAC
66 ATGAAATCTTGATAACTAC
* ** * * * *
36410 AAATTTTGAT-AACCTCCCTATGATTTTTTGAT-AACCTCATTATGAAATTTTGTTAATCTCCCT
1 AAATTTTGATAAACCTCCCTATAAAATTTTGATAAACCTCACTATAAAATTTTGATAACCTCCCT
*
36473 ATGAAATTTTGATAAC
66 ATGAAATCTTGATAAC
36489 CCTCTTATGA
Statistics
Matches: 67, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
82 39 0.58
83 18 0.27
84 10 0.15
ACGTcount: A:0.35, C:0.17, G:0.07, T:0.40
Consensus pattern (84 bp):
AAATTTTGATAAACCTCCCTATAAAATTTTGATAAACCTCACTATAAAATTTTGATAACCTCCCT
ATGAAATCTTGATAACTAC
Found at i:36486 original size:104 final size:106
Alignment explanation
Indices: 36304--36512 Score: 273
Period size: 104 Copynumber: 2.0 Consensus size: 106
36294 TCACACTCTG
* *
36304 AAATTATGATAATCTCGCTATGAAATTTTGATAAACCTTCCTATAAAATTTTGATAAATCTCCCT
1 AAATTATGATAACCTCCCTATGAAATTTTGATAAACCTTCCTATAAAATTTTGATAAATCTCCCT
*
36369 ATAAAATTTTGATAA-CCTCCTTATGAAATCTTGATAACTAC
66 ATAAAATTTTGATAACCCT-CTTATGAAATCTTGAAAACTAC
* ** * * *
36410 AAATTTTGATAACCTCCCTATGATTTTTTGAT-AACC-TCATTATGAAATTTTG-TTAATCTCCC
1 AAATTATGATAACCTCCCTATGAAATTTTGATAAACCTTC-CTATAAAATTTTGATAAATCTCCC
* *
36472 TATGAAATTTTGATAACCCTCTTATGAAATTTTGAAAACTA
65 TATAAAATTTTGATAACCCTCTTATGAAATCTTGAAAACTA
36513 AACTATGAAG
Statistics
Matches: 90, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
104 45 0.50
105 18 0.20
106 27 0.30
ACGTcount: A:0.35, C:0.17, G:0.08, T:0.40
Consensus pattern (106 bp):
AAATTATGATAACCTCCCTATGAAATTTTGATAAACCTTCCTATAAAATTTTGATAAATCTCCCT
ATAAAATTTTGATAACCCTCTTATGAAATCTTGAAAACTAC
Found at i:36635 original size:22 final size:21
Alignment explanation
Indices: 36114--36639 Score: 263
Period size: 22 Copynumber: 24.4 Consensus size: 21
36104 ATAATTTTTT
* *
36114 TAACCTTCTTATGAAATTTTGT
1 TAACC-TCCTATGAAATTTTGA
* *
36136 TAACCTCCCTAAGGAATTTTGA
1 TAACCT-CCTATGAAATTTTGA
36158 -AGACCTCACTATGAAATTTTGA
1 TA-ACCTC-CTATGAAATTTTGA
* *
36180 TAACTTCCAAATGAAATTTTGA
1 TAACCTCC-TATGAAATTTTGA
* *
36202 TAACCAACACTAT-AAGATATTGA
1 TAACC-TC-CTATGAA-ATTTTGA
* *
36225 TAACCTCCATATGATATATTGA
1 TAACCTCC-TATGAAATTTTGA
* * * *
36247 TAACCACGGTATGAAAATTTAA
1 TAACCTC-CTATGAAATTTTGA
* * *
36269 AAACCTCCATATG-AATTGTCA
1 TAACCTCC-TATGAAATTTTGA
* * * *
36290 GTAATCACACTCTGAAATTATGA
1 -TAACCTC-CTATGAAATTTTGA
*
36313 TAATCTCGCTATGAAATTTTGA
1 TAACCTC-CTATGAAATTTTGA
*
36335 TAAACCTTCCTATAAAATTTTGA
1 T-AACC-TCCTATGAAATTTTGA
* *
36358 TAAATCTCCCTATAAAATTTTGA
1 T-AACCT-CCTATGAAATTTTGA
*
36381 TAACCTCCTTATGAAATCTTGA
1 TAACCTCC-TATGAAATTTTGA
*
36403 TAA----CTA-CAAATTTTGA
1 TAACCTCCTATGAAATTTTGA
**
36419 TAACCTCCCTATGATTTTTTGA
1 TAACCT-CCTATGAAATTTTGA
* *
36441 TAACCTCATTATGAAATTTTGT
1 TAACCTC-CTATGAAATTTTGA
*
36463 TAATCTCCCTATGAAATTTTGA
1 TAACCT-CCTATGAAATTTTGA
*
36485 TAACCCTCTTATGAAATTTTGA
1 TAA-CCTCCTATGAAATTTTGA
* * *
36507 -AAACTAAACTATGAAGTTTTGA
1 TAACCT--CCTATGAAATTTTGA
* *
36529 TAACCTTCATATTAAATTTTGA
1 TAACC-TCCTATGAAATTTTGA
* *
36551 TATCCTCC-CTGAAATTTTGA
1 TAACCTCCTATGAAATTTTGA
* * * *
36571 TTA-CTCCATAATAAAAGTTTAA
1 TAACCTCC-T-ATGAAATTTTGA
* *
36593 TAACCTTCT-T--AA-TTTGG
1 TAACCTCCTATGAAATTTTGA
*
36610 TAACCATACTATGAAATTTTGA
1 TAACC-TCCTATGAAATTTTGA
36632 TAACCTCC
1 TAACCTCC
36640 CCAGAAATAC
Statistics
Matches: 381, Mismatches: 82, Indels: 83
0.70 0.15 0.15
Matches are distributed among these distances:
16 11 0.03
17 10 0.03
18 6 0.02
19 5 0.01
20 14 0.04
21 24 0.06
22 238 0.62
23 69 0.18
24 4 0.01
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.37
Consensus pattern (21 bp):
TAACCTCCTATGAAATTTTGA
Found at i:36702 original size:22 final size:22
Alignment explanation
Indices: 36653--36797 Score: 129
Period size: 22 Copynumber: 6.6 Consensus size: 22
36643 GAAATACCAC
* * *
36653 TATGAAATTTTGGTAATCACATT
1 TATGAAATTTTGATAACCTC-TT
*
36676 T-TGAAAATTTGATAACCTCTT
1 TATGAAATTTTGATAACCTCTT
36697 TATGAAATTTTGATAACCTCTT
1 TATGAAATTTTGATAACCTCTT
* * *
36719 TAT-AAATTTTTGTTGACCACTT
1 TATGAAA-TTTTGATAACCTCTT
36741 TATGAAATTTTGATAA--TCATAT
1 TATGAAATTTTGATAACCTC-T-T
* *
36763 TATGTAATTTTGATAACCTCGCT
1 TATGAAATTTTGATAACCTC-TT
36786 T-TGAAATTTTGA
1 TATGAAATTTTGA
36798 AATTGGACCA
Statistics
Matches: 100, Mismatches: 15, Indels: 15
0.77 0.12 0.12
Matches are distributed among these distances:
20 1 0.01
21 7 0.07
22 84 0.84
23 6 0.06
24 2 0.02
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCTT
Found at i:36703 original size:44 final size:44
Alignment explanation
Indices: 36653--36797 Score: 143
Period size: 44 Copynumber: 3.3 Consensus size: 44
36643 GAAATACCAC
* *
36653 TATGAAATTTTGGTAATCACATTTTGAAAATTTGATAACCTCTT
1 TATGAAATTTTGATAATCACATTTTGAAATTTTGATAACCTCTT
* * * * *
36697 TATGAAATTTTGATAACCTC-TTTAT-AAATTTTTGTTGACCACTT
1 TATGAAATTTTGATAATCACATTT-TGAAA-TTTTGATAACCTCTT
* * * *
36741 TATGAAATTTTGATAATCATATTATGTAATTTTGATAACCTCGCT
1 TATGAAATTTTGATAATCACATTTTGAAATTTTGATAACCTC-TT
36786 T-TGAAATTTTGA
1 TATGAAATTTTGA
36798 AATTGGACCA
Statistics
Matches: 80, Mismatches: 16, Indels: 10
0.75 0.15 0.09
Matches are distributed among these distances:
43 6 0.08
44 68 0.85
45 6 0.08
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (44 bp):
TATGAAATTTTGATAATCACATTTTGAAATTTTGATAACCTCTT
Found at i:36921 original size:37 final size:37
Alignment explanation
Indices: 36862--36950 Score: 92
Period size: 37 Copynumber: 2.4 Consensus size: 37
36852 CCCAAATAGG
*
36862 ACGTTGGAGACTAAGAGA-AAAAG-CAAAATAAAATACA
1 ACGTTGGAAAC-AA-AGACAAAAGACAAAATAAAATACA
* * **
36899 ACGATTGGAAACAAAGACAAAAGATAAAATTAAATAGG
1 ACG-TTGGAAACAAAGACAAAAGACAAAATAAAATACA
36937 ACGTTGGAAACAAA
1 ACGTTGGAAACAAA
36951 AAGTCAAATT
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
36 3 0.07
37 21 0.48
38 20 0.45
ACGTcount: A:0.56, C:0.10, G:0.19, T:0.15
Consensus pattern (37 bp):
ACGTTGGAAACAAAGACAAAAGACAAAATAAAATACA
Found at i:37020 original size:26 final size:26
Alignment explanation
Indices: 36991--37050 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
36981 TACGTATTAT
*
36991 ATAATCTAATAATT-AATAATAATGGA
1 ATAAT-TAATAATTAAAAAATAATGGA
* *
37017 ATAATTTATGATTAAAAAATAATGGA
1 ATAATTAATAATTAAAAAATAATGGA
37043 ATAATTAA
1 ATAATTAA
37051 AATATTGTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 6 0.21
26 23 0.79
ACGTcount: A:0.55, C:0.02, G:0.08, T:0.35
Consensus pattern (26 bp):
ATAATTAATAATTAAAAAATAATGGA
Found at i:37104 original size:32 final size:32
Alignment explanation
Indices: 37068--37135 Score: 104
Period size: 31 Copynumber: 2.2 Consensus size: 32
37058 TTTAGTAATA
37068 ACAATTTAGAAATATATTTTCAAAAA-AAGGGT
1 ACAATTTAGAAATATATTTT-AAAAATAAGGGT
*
37100 ACAA-TTGGAAATATATTTTAAAAATAAGGGT
1 ACAATTTAGAAATATATTTTAAAAATAAGGGT
37131 ACAAT
1 ACAAT
37136 CGAAAAACAT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
30 5 0.15
31 24 0.73
32 4 0.12
ACGTcount: A:0.50, C:0.06, G:0.13, T:0.31
Consensus pattern (32 bp):
ACAATTTAGAAATATATTTTAAAAATAAGGGT
Found at i:37442 original size:19 final size:20
Alignment explanation
Indices: 37401--37442 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
37391 GTAGTGGGGG
**
37401 AAAGAAAAAGTAAAGAATTA
1 AAAGAAAAAGTAAAGAAAGA
*
37421 AAAGGAAAA-TAAAGAAAGA
1 AAAGAAAAAGTAAAGAAAGA
37440 AAA
1 AAA
37443 AAGACAATGT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.74, C:0.00, G:0.17, T:0.10
Consensus pattern (20 bp):
AAAGAAAAAGTAAAGAAAGA
Found at i:40899 original size:13 final size:13
Alignment explanation
Indices: 40881--40909 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
40871 AGGGGTGATT
40881 AAAAAAAAGAAAA
1 AAAAAAAAGAAAA
40894 AAAAAAAAGAAAA
1 AAAAAAAAGAAAA
40907 AAA
1 AAA
40910 CAGAGTACGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (13 bp):
AAAAAAAAGAAAA
Found at i:47072 original size:1 final size:1
Alignment explanation
Indices: 47066--47108 Score: 68
Period size: 1 Copynumber: 43.0 Consensus size: 1
47056 CTGAGGTTAG
* *
47066 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTTTCTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
47109 ATATATATAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
1 38 1.00
ACGTcount: A:0.00, C:0.05, G:0.00, T:0.95
Consensus pattern (1 bp):
T
Found at i:48779 original size:9 final size:9
Alignment explanation
Indices: 48765--48792 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
48755 AGCCATATAT
48765 ATATCATTA
1 ATATCATTA
48774 ATATCATTA
1 ATATCATTA
48783 ATATCATTA
1 ATATCATTA
48792 A
1 A
48793 GCTGCTTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (9 bp):
ATATCATTA
Found at i:78494 original size:8 final size:8
Alignment explanation
Indices: 78483--78518 Score: 54
Period size: 8 Copynumber: 4.2 Consensus size: 8
78473 ATTAAAAATT
78483 AAAAAGGA
1 AAAAAGGA
78491 AAAAAGGA
1 AAAAAGGA
78499 AAAAAGGA
1 AAAAAGGA
78507 AGAAAAGAGA
1 A-AAAAG-GA
78517 AA
1 AA
78519 CAAATTAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
8 17 0.65
9 6 0.23
10 3 0.12
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (8 bp):
AAAAAGGA
Found at i:84831 original size:54 final size:56
Alignment explanation
Indices: 84728--84834 Score: 164
Period size: 54 Copynumber: 1.9 Consensus size: 56
84718 TCATTTAACG
**
84728 ACAACAATTAACATATGCAAAACAAAATTATATATAGCATCAGCACTAAACAACAACA
1 ACAACAACCAACATATGCAAAAC--AATTATATATAGCATCAGCACTAAACAACAACA
84786 ACAACAACCAACATATGCAAAAC-A-TATATATAGCATCAGCACTAAACAA
1 ACAACAACCAACATATGCAAAACAATTATATATAGCATCAGCACTAAACAA
84835 TTCAATTGCA
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
54 25 0.53
55 1 0.02
58 21 0.45
ACGTcount: A:0.54, C:0.22, G:0.06, T:0.18
Consensus pattern (56 bp):
ACAACAACCAACATATGCAAAACAATTATATATAGCATCAGCACTAAACAACAACA
Found at i:90796 original size:163 final size:163
Alignment explanation
Indices: 90582--90906 Score: 519
Period size: 163 Copynumber: 2.0 Consensus size: 163
90572 AGCCAGCCCA
*
90582 CTAGCTTTTTTTTTTTAAAGGAAATAATCATTTTCATTTCTTGATTTGAGATTAACCCAACAAAT
1 CTAGCTTTTTTTTTTT-AAGGAAAGAATCATTTTCATTTCTTGATTTGAGATTAACCCAACAAAT
* * *
90647 AAA-CTCAGTGAAATTTTATAACAATTCAAATAAATTTTTATACCCATAAATAAACTACATACCT
65 AAACCT-AGTGAAATCTCATAACAATTCAAATAAATCTTTATACCCATAAATAAACTACATACCT
90711 ACCAAATACATAAATAAACAAACTACAAATAAATT
129 ACCAAATACATAAATAAACAAACTACAAATAAATT
* *
90746 CTAGCTTCTTTTTTTTT-AGGAAAGAATCATTTTCATTTCTTGATTTGAGATTAGCCCAACGAAT
1 CTAGCTT-TTTTTTTTTAAGGAAAGAATCATTTTCATTTCTTGATTTGAGATTAACCCAACAAAT
* *
90810 AAACCTAGTGAAATCTCGTAACAATTCAAATAAATCTTTATACTCATAAATAAACTACATACCTA
65 AAACCTAGTGAAATCTCATAACAATTCAAATAAATCTTTATACCCATAAATAAACTACATACCTA
* *
90875 TCAAATACATAAATAAACAAATTACAAATAAA
130 CCAAATACATAAATAAACAAACTACAAATAAA
90907 CTCACATTCC
Statistics
Matches: 149, Mismatches: 10, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
163 131 0.88
164 9 0.06
165 9 0.06
ACGTcount: A:0.43, C:0.16, G:0.06, T:0.34
Consensus pattern (163 bp):
CTAGCTTTTTTTTTTTAAGGAAAGAATCATTTTCATTTCTTGATTTGAGATTAACCCAACAAATA
AACCTAGTGAAATCTCATAACAATTCAAATAAATCTTTATACCCATAAATAAACTACATACCTAC
CAAATACATAAATAAACAAACTACAAATAAATT
Found at i:93189 original size:18 final size:19
Alignment explanation
Indices: 93166--93204 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
93156 ATGAACAGAT
*
93166 TTTTGAGTCTT-GATTTGA
1 TTTTGAGTCTTCCATTTGA
*
93184 TTTTGATTCTTCCATTTGA
1 TTTTGAGTCTTCCATTTGA
93203 TT
1 TT
93205 ATTTTATTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.15, C:0.10, G:0.15, T:0.59
Consensus pattern (19 bp):
TTTTGAGTCTTCCATTTGA
Found at i:95533 original size:21 final size:20
Alignment explanation
Indices: 95504--95546 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
95494 AGAGGATCTA
95504 TTTTTAACATCCTAGCACGT
1 TTTTTAACATCCTAGCACGT
*
95524 TTTTCTAACATCCTCGCACGT
1 TTTT-TAACATCCTAGCACGT
95545 TT
1 TT
95547 GGAATTCCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.21, C:0.28, G:0.09, T:0.42
Consensus pattern (20 bp):
TTTTTAACATCCTAGCACGT
Found at i:97974 original size:22 final size:22
Alignment explanation
Indices: 97949--98505 Score: 183
Period size: 22 Copynumber: 25.6 Consensus size: 22
97939 ATGATCCCAT
97949 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCTTCC
* *** *
97971 TATGAAATTTTAATAATGATAC
1 TATGAAATTTTGATAACCTTCC
* * * **
97993 TACG-AATTTCGAGAACCTTTT
1 TATGAAATTTTGATAACCTTCC
** **
98014 TAT-AAATTATTTTTAACCTTTT
1 TATGAAATT-TTGATAACCTTCC
* *
98036 TATGAAATTTTGTTAACCTCCC
1 TATGAAATTTTGATAACCTTCC
* * *
98058 TAAGTAATTTTGA-AGACC-TCAA
1 TATGAAATTTTGATA-ACCTTC-C
98080 TATGAAATTTTGATAA-CTTCCC
1 TATGAAATTTTGATAACCTT-CC
* * **
98102 AATGAAATTTTTATAACCAACAC
1 TATGAAATTTTGATAACCTTC-C
*
98125 TATGAAATGTTGATAACC-TCC
1 TATGAAATTTTGATAACCTTCC
* * * *
98146 ATATGATATATTGATAACC-ACGT
1 -TATGAAATTTTGATAACCTTC-C
* * * *
98169 TAAGAAAATTTAAAAACC-TCC
1 TATGAAATTTTGATAACCTTCC
* *
98190 GTATG-AATTGTT-AGTAATC-ACAC
1 -TATGAAATT-TTGA-TAACCTTC-C
* * * *
98213 TTTTAAATTTTGATAATC-ACAC
1 TATGAAATTTTGATAACCTTC-C
*
98235 TATGAAATTGTGATAACC-TCGC
1 TATGAAATTTTGATAACCTTC-C
* * *
98257 TACGAAATTTTGATAAATCTACC
1 TATGAAATTTTGAT-AACCTTCC
* * * *
98280 TA-AAAATTTTTGATAGCTTTCT
1 TATGAAA-TTTTGATAACCTTCC
*
98302 TATGAAATCTTGATAA-----C
1 TATGAAATTTTGATAACCTTCC
* *
98319 TA-CAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTTCC
** *
98340 TATGATTTTTTGATAACC-TCAT
1 TATGAAATTTTGATAACCTTC-C
* * *
98362 TATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCTTCC
* * *
98384 TATGAAATTTTGATCTA-CATAC
1 TATGAAATTTTGAT-AACCTTCC
* *
98406 TATGAAATTTTGATAACCCTCT
1 TATGAAATTTTGATAACCTTCC
* **
98428 TATGAAATTTTGA-AAACTAAAC
1 TATGAAATTTTGATAACCT-TCC
*
98450 TATGAAATTTTGATAACCTTCA
1 TATGAAATTTTGATAACCTTCC
*
98472 TATGAAATTTTGATATCC-TCC
1 TATGAAATTTTGATAACCTTCC
*
98493 -CTGAAATTTTGAT
1 TATGAAATTTTGAT
98506 TACTCCATAA
Statistics
Matches: 389, Mismatches: 112, Indels: 70
0.68 0.20 0.12
Matches are distributed among these distances:
16 11 0.03
17 2 0.01
20 12 0.03
21 33 0.08
22 278 0.71
23 52 0.13
24 1 0.00
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Found at i:98163 original size:45 final size:45
Alignment explanation
Indices: 98080--98165 Score: 111
Period size: 45 Copynumber: 1.9 Consensus size: 45
98070 AAGACCTCAA
* * * *
98080 TATGAAATTTTGATAACTTCCCAATGAAATTTTTATAACCAACAC
1 TATGAAATGTTGATAACCTCCCAATGAAATATTGATAACCAACAC
*
98125 TATGAAATGTTGATAACCT-CCATATGATATATTGATAACCA
1 TATGAAATGTTGATAACCTCCCA-ATGAAATATTGATAACCA
98166 CGTTAAGAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
44 3 0.09
45 32 0.91
ACGTcount: A:0.40, C:0.16, G:0.09, T:0.35
Consensus pattern (45 bp):
TATGAAATGTTGATAACCTCCCAATGAAATATTGATAACCAACAC
Found at i:98682 original size:22 final size:22
Alignment explanation
Indices: 98611--98982 Score: 116
Period size: 22 Copynumber: 16.6 Consensus size: 22
98601 AATCACATTT
* * * *
98611 TGAAAATTTGAAAACCTCTTTA
1 TGAAATTTTGATAACCCCTCTA
* *
98633 TGAAATTTTGATAACCTCTTTA
1 TGAAATTTTGATAACCCCTCTA
* * *
98655 TAAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAACCCCTCTA
* ** *
98677 TGAAATTCTGATAATGACAT-TA
1 TGAAATTTTGATAA-CCCCTCTA
* * * * *
98699 TGTAATTTTGATAATCTCGCTT
1 TGAAATTTTGATAACCCCTCTA
** *
98721 TGAAATTTTGATAACAACACTA
1 TGAAATTTTGATAACCCCTCTA
**
98743 TGAAATTTTGATAATCTGATCTCTA
1 TGAAATTTTGATAA-C--CCCTCTA
* * * *
98768 TGAAATTTCGATAATCACTTTA
1 TGAAATTTTGATAACCCCTCTA
* *
98790 TGAGA-TTTGATAA-CCTTCTA
1 TGAAATTTTGATAACCCCTCTA
* * *
98810 TCAAATTTTGGT-ACTCCT-TA
1 TGAAATTTTGATAACCCCTCTA
* **
98830 TGAAATTGAGACTTTTTATAA-CTTTCATA
1 TG--A---A-A-TTTTGATAACCCCTC-TA
* *
98859 TGAAATTTTGATAACCACACTA
1 TGAAATTTTGATAACCCCTCTA
*
98881 TAAAATTTTGATAACCTCCTC-A
1 TGAAATTTTGATAACC-CCTCTA
* *
98903 TGAAATATT-AGTAACCTCT-TAA
1 TGAAATTTTGA-TAACCCCTCT-A
* * *
98925 TGAAATTTTGTTAACCACACTA
1 TGAAATTTTGATAACCCCTCTA
* *
98947 TGAAATTCTT-ATAACCTCGCTA
1 TGAAATT-TTGATAACCCCTCTA
*
98969 TGACATTTTGATAA
1 TGAAATTTTGATAA
98983 TCTCTTTGAT
Statistics
Matches: 255, Mismatches: 69, Indels: 52
0.68 0.18 0.14
Matches are distributed among these distances:
20 11 0.04
21 19 0.07
22 181 0.71
23 11 0.04
24 1 0.00
25 19 0.07
26 1 0.00
27 7 0.03
28 1 0.00
29 4 0.02
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (22 bp):
TGAAATTTTGATAACCCCTCTA
Found at i:98727 original size:66 final size:66
Alignment explanation
Indices: 98630--98757 Score: 150
Period size: 66 Copynumber: 1.9 Consensus size: 66
98620 GAAAACCTCT
* * * ** *
98630 TTATGAAATTTTGATAACCTCTTTATAAAATTTTGTTGACCCCTCTATGAAATTCTGATAATGAC
1 TTATGAAATTTTGATAACCTCCTTATAAAATTTTGATAACAACACTATGAAATTCTGATAATGAC
98695 A
66 A
* * * *
98696 TTATGTAATTTTGATAATCTCGCTT-TGAAATTTTGATAACAACACTATGAAATTTTGATAAT
1 TTATGAAATTTTGATAACCTC-CTTATAAAATTTTGATAACAACACTATGAAATTCTGATAAT
98758 CTGATCTCTA
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
66 49 0.96
67 2 0.04
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.42
Consensus pattern (66 bp):
TTATGAAATTTTGATAACCTCCTTATAAAATTTTGATAACAACACTATGAAATTCTGATAATGAC
A
Found at i:99100 original size:22 final size:22
Alignment explanation
Indices: 99026--99223 Score: 152
Period size: 22 Copynumber: 8.9 Consensus size: 22
99016 ATTAACCACC
** *
99026 CTATGAAATTTCAATAATCA-A
1 CTATGAAATTTTGATAACCATA
* * *
99047 CCTAAGAAATTTTAATAACCTGATC
1 -CTATGAAATTTTGATAACC--ATA
*
99072 CTATGAAATTTTGGTAACCATA
1 CTATGAAATTTTGATAACCATA
* *
99094 CTATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGATAACCATA
* *
99116 CTATGAAATTTTGATAA-CTTC
1 CTATGAAATTTTGATAACCATA
* *
99137 CATATGAAATTTTGGTAACCACA
1 C-TATGAAATTTTGATAACCATA
** *
99160 CTATGTTATTTTGATAACC-TC
1 CTATGAAATTTTGATAACCATA
* *
99181 CTCATGAAATTATAATAACCAT-
1 CT-ATGAAATTTTGATAACCATA
99203 CTTATGAAATTTTGATAACCA
1 C-TATGAAATTTTGATAACCA
99224 AATAGAGACA
Statistics
Matches: 140, Mismatches: 28, Indels: 16
0.76 0.15 0.09
Matches are distributed among these distances:
21 4 0.03
22 115 0.82
23 4 0.03
24 17 0.12
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.36
Consensus pattern (22 bp):
CTATGAAATTTTGATAACCATA
Found at i:99128 original size:44 final size:44
Alignment explanation
Indices: 99018--99223 Score: 177
Period size: 44 Copynumber: 4.6 Consensus size: 44
99008 TTGTGATAAT
* ** * * * **
99018 TAACCACCCTATGAAATTTCAATAATCAACCTAAGAAATTTTAA
1 TAACCACACTATGAAATTTTGATAACCATCCTATGAAATTTTGG
* *
99062 TAACCTGATC-CTATGAAATTTTGGTAACCATACTATGAAATTTTGG
1 TAACC--A-CACTATGAAATTTTGATAACCATCCTATGAAATTTTGG
*
99108 TAACCACACTATGAAATTTTGATAA-CTTCCATATGAAATTTTGG
1 TAACCACACTATGAAATTTTGATAACCATCC-TATGAAATTTTGG
** * **
99152 TAACCACACTATGTTATTTTGATAACC-TCCTCATGAAATTATAA
1 TAACCACACTATGAAATTTTGATAACCATCCT-ATGAAATTTTGG
*
99196 TAACCATC-TTATGAAATTTTGATAACCA
1 TAACCA-CACTATGAAATTTTGATAACCA
99224 AATAGAGACA
Statistics
Matches: 133, Mismatches: 20, Indels: 17
0.78 0.12 0.10
Matches are distributed among these distances:
43 5 0.04
44 92 0.69
45 2 0.02
46 33 0.25
47 1 0.01
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.35
Consensus pattern (44 bp):
TAACCACACTATGAAATTTTGATAACCATCCTATGAAATTTTGG
Found at i:99163 original size:66 final size:66
Alignment explanation
Indices: 99018--99223 Score: 193
Period size: 66 Copynumber: 3.1 Consensus size: 66
99008 TTGTGATAAT
* ** * * * *
99018 TAACCACCCTATGAAATTTCAATAATCAACCT-AAGAAATTTTAATAACCTGATCCTATGAAATT
1 TAACCACACTATGAAATTTTGATAA-CCACCTCATGAAATTATAATAACC--ATCATATGAAATT
99082 TTGG
63 TTGG
* * * * *
99086 TAACCATACTATGAAATTTTGGTAACCACACT-ATGAAATTTTGATAA-CTTCCATATGAAATTT
1 TAACCACACTATGAAATTTTGATAACCAC-CTCATGAAATTATAATAACCAT-CATATGAAATTT
99149 TGG
64 TGG
** * *
99152 TAACCACACTATGTTATTTTGATAACCTCCTCATGAAATTATAATAACCATCTTATGAAATTTTG
1 TAACCACACTATGAAATTTTGATAACCACCTCATGAAATTATAATAACCATCATATGAAATTTTG
*
99217 A
66 G
99218 TAACCA
1 TAACCA
99224 AATAGAGACA
Statistics
Matches: 114, Mismatches: 20, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
65 3 0.03
66 70 0.61
67 6 0.05
68 35 0.31
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.35
Consensus pattern (66 bp):
TAACCACACTATGAAATTTTGATAACCACCTCATGAAATTATAATAACCATCATATGAAATTTTG
G
Found at i:99412 original size:19 final size:20
Alignment explanation
Indices: 99388--99431 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
99378 TTATTGACAT
99388 TTAAAA-ATTGAAATT-AAAA
1 TTAAAATATT-AAATTAAAAA
99407 TTAAAATATTAAATTCAAAAA
1 TTAAAATATTAAATT-AAAAA
99428 TTAA
1 TTAA
99432 TAGTAAAGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 11 0.50
20 3 0.14
21 8 0.36
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (20 bp):
TTAAAATATTAAATTAAAAA
Found at i:99573 original size:38 final size:37
Alignment explanation
Indices: 99518--99614 Score: 133
Period size: 38 Copynumber: 2.6 Consensus size: 37
99508 AATTAATTTT
* * *
99518 TAAATAGGACGTTGGAAACAAAGACAAAAAGCAAAAT
1 TAAATAAGACGTTGGAAACAAAGACAAAAAGAAAAAA
*
99555 TAAATACA-ACGATTGGAAACAAAGACAAAAGGAAAAAA
1 TAAATA-AGACG-TTGGAAACAAAGACAAAAAGAAAAAA
99593 TAAATAAGACGTTGGAAACAAA
1 TAAATAAGACGTTGGAAACAAA
99615 AAGGCAAATT
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
37 21 0.40
38 32 0.60
ACGTcount: A:0.59, C:0.10, G:0.18, T:0.13
Consensus pattern (37 bp):
TAAATAAGACGTTGGAAACAAAGACAAAAAGAAAAAA
Found at i:99795 original size:31 final size:31
Alignment explanation
Indices: 99737--99802 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
99727 TGGCAATTTA
** *
99737 GAAATATGTTTTTAAAAAAAGGGTACAATTG
1 GAAATATGTTTTTAAAAAAAGAATACAATCG
*
99768 GAAATATG-TTTTAAATATAAGAATACAATCG
1 GAAATATGTTTTTAAA-AAAAGAATACAATCG
99799 GAAA
1 GAAA
99803 ACATAAAGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 7 0.23
31 23 0.77
ACGTcount: A:0.48, C:0.05, G:0.17, T:0.30
Consensus pattern (31 bp):
GAAATATGTTTTTAAAAAAAGAATACAATCG
Found at i:99855 original size:21 final size:20
Alignment explanation
Indices: 99829--99870 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 20
99819 TATTCGTACT
99829 TTTATATA-TAGTATAGATATA
1 TTTATATATTA-TATA-ATATA
99850 TTTATATATTATATAATATA
1 TTTATATATTATATAATATA
99870 T
1 T
99871 ATTAATTTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 6 0.30
21 12 0.60
22 2 0.10
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (20 bp):
TTTATATATTATATAATATA
Found at i:101197 original size:35 final size:35
Alignment explanation
Indices: 101151--101224 Score: 112
Period size: 35 Copynumber: 2.1 Consensus size: 35
101141 TCAATGACTT
*
101151 AACCCTAAAAACCATAGATCAAGACCTACGAAATA
1 AACCCTAAAAACAATAGATCAAGACCTACGAAATA
* * *
101186 AACCCTAAAAACAATAGCTCAAGATCTGCGAAATA
1 AACCCTAAAAACAATAGATCAAGACCTACGAAATA
101221 AACC
1 AACC
101225 TTTACGGAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.50, C:0.26, G:0.09, T:0.15
Consensus pattern (35 bp):
AACCCTAAAAACAATAGATCAAGACCTACGAAATA
Found at i:102598 original size:18 final size:19
Alignment explanation
Indices: 102575--102613 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
102565 TCGACTTCAT
102575 TAGATTCCGAG-ATTCCAA
1 TAGATTCCGAGAATTCCAA
**
102593 TAGATTTTGAGAATTCCAA
1 TAGATTCCGAGAATTCCAA
102612 TA
1 TA
102614 ACACCACACC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.33
Consensus pattern (19 bp):
TAGATTCCGAGAATTCCAA
Found at i:105513 original size:5 final size:5
Alignment explanation
Indices: 105512--105540 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
105502 TTAATATAAT
105512 ATATA ATATA ATATA ATATA ATAT- ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA
105541 CTAGTTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
ATATA
Found at i:105520 original size:12 final size:12
Alignment explanation
Indices: 105503--105538 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
105493 TTAGGATTCT
105503 TAATATAATATA
1 TAATATAATATA
105515 TAATAT-A-ATA
1 TAATATAATATA
105525 TAATATAATATA
1 TAATATAATATA
105537 TA
1 TA
105539 TACTAGTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 9 0.41
11 2 0.09
12 11 0.50
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
TAATATAATATA
Found at i:106695 original size:110 final size:112
Alignment explanation
Indices: 106500--106718 Score: 370
Period size: 110 Copynumber: 2.0 Consensus size: 112
106490 ATTTTGGCCG
106500 ATAATGGACCGAATTTAAGTTAGTGTGGAAAAAGGAAAAAAGAAAAGAAATTGAACTAAAAAGCC
1 ATAATGGACCGAATTTAAGTTAGTGTGGAAAAAGGAAAAAAGAAAAGAAATTGAACTAAAAAGCC
** *
106565 AGCGTGGCTTAATTAGGAAGCTCTATTTTGTATGAGCTTTTATAATA
66 AAAGTGGCTTAATGAGGAAGCTCTATTTTGTATGAGCTTTTATAATA
* * *
106612 ATAATGGGCCGAATTTAAGTTGGTGTGGAAAAAGG-AAAAA-AAAAGAAATTGAATTAAAAAGCC
1 ATAATGGACCGAATTTAAGTTAGTGTGGAAAAAGGAAAAAAGAAAAGAAATTGAACTAAAAAGCC
106675 AAAGTGGCTTAATGAGGAAGCTCTATTTTGTATGAGCTTTTATA
66 AAAGTGGCTTAATGAGGAAGCTCTATTTTGTATGAGCTTTTATA
106719 TATAGTATAA
Statistics
Matches: 101, Mismatches: 6, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
110 63 0.62
111 5 0.05
112 33 0.33
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (112 bp):
ATAATGGACCGAATTTAAGTTAGTGTGGAAAAAGGAAAAAAGAAAAGAAATTGAACTAAAAAGCC
AAAGTGGCTTAATGAGGAAGCTCTATTTTGTATGAGCTTTTATAATA
Found at i:108314 original size:15 final size:14
Alignment explanation
Indices: 108266--108317 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 14
108256 ATGATTTTCA
*
108266 ATTATTTATTAAATT
1 ATTATTT-TTAATTT
* *
108281 ATTAATTATACATTT
1 ATTATTTTTA-ATTT
108296 ATTATTTTTAATTT
1 ATTATTTTTAATTT
108310 AATTATTT
1 -ATTATTT
108318 ATTTTTATAG
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
14 6 0.20
15 24 0.80
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (14 bp):
ATTATTTTTAATTT
Found at i:112182 original size:29 final size:30
Alignment explanation
Indices: 112128--112196 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 30
112118 TTATAACTTA
* *
112128 AAAAGTAAGGTTCAACTGAAGTGGAAA-GAAC
1 AAAAG-AA-GTTCAACGGAAGGGGAAACGAAC
*
112159 TAAAGAAGTTCAACGGAAGGGGAAACGAAC
1 AAAAGAAGTTCAACGGAAGGGGAAACGAAC
112189 AAAAGAAG
1 AAAAGAAG
112197 AGCTAGATGA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 16 0.48
30 13 0.39
31 4 0.12
ACGTcount: A:0.51, C:0.10, G:0.28, T:0.12
Consensus pattern (30 bp):
AAAAGAAGTTCAACGGAAGGGGAAACGAAC
Found at i:112509 original size:12 final size:12
Alignment explanation
Indices: 112492--112525 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
112482 CTCTAACAAG
112492 CTCACACA-ATCT
1 CTCACACACA-CT
112504 CTCACACACACT
1 CTCACACACACT
112516 CTCACACACA
1 CTCACACACA
112526 AAAAAAACTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 20 0.95
13 1 0.05
ACGTcount: A:0.35, C:0.47, G:0.00, T:0.18
Consensus pattern (12 bp):
CTCACACACACT
Found at i:113944 original size:23 final size:23
Alignment explanation
Indices: 113918--113962 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
113908 TTGCTAGTTC
*
113918 ATAGAGATCGAGCGAAAGTGCTT
1 ATAGAGACCGAGCGAAAGTGCTT
*
113941 ATAGAGACCGAGCGAGAGTGCT
1 ATAGAGACCGAGCGAAAGTGCT
113963 CAAGATTGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.33, C:0.16, G:0.33, T:0.18
Consensus pattern (23 bp):
ATAGAGACCGAGCGAAAGTGCTT
Found at i:116813 original size:15 final size:14
Alignment explanation
Indices: 116790--116824 Score: 61
Period size: 14 Copynumber: 2.4 Consensus size: 14
116780 TCAAAATAAA
116790 AACCGAAAAAACCG
1 AACCGAAAAAACCG
116804 AACCGAAAAAACCG
1 AACCGAAAAAACCG
116818 ACACCGA
1 A-ACCGA
116825 CCGACACCGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 15 0.75
15 5 0.25
ACGTcount: A:0.54, C:0.31, G:0.14, T:0.00
Consensus pattern (14 bp):
AACCGAAAAAACCG
Found at i:121810 original size:11 final size:10
Alignment explanation
Indices: 121785--121809 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
121775 CTAACTTTTC
121785 TTTTTCTTAT
1 TTTTTCTTAT
121795 TTTTTCTTAT
1 TTTTTCTTAT
121805 TTTTT
1 TTTTT
121810 TTTGGGGCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.84
Consensus pattern (10 bp):
TTTTTCTTAT
Found at i:128600 original size:11 final size:11
Alignment explanation
Indices: 128586--128611 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
128576 AATCCTATCC
128586 AAATTCCCAAT
1 AAATTCCCAAT
128597 AAATTCCCAAT
1 AAATTCCCAAT
128608 AAAT
1 AAAT
128612 AATTTGGTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (11 bp):
AAATTCCCAAT
Found at i:145830 original size:15 final size:15
Alignment explanation
Indices: 145810--145839 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
145800 CATCACTAAT
145810 AAAGTAGGAAGAAGC
1 AAAGTAGGAAGAAGC
145825 AAAGTAGGAAGAAGC
1 AAAGTAGGAAGAAGC
145840 TTGAAATCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.07, G:0.33, T:0.07
Consensus pattern (15 bp):
AAAGTAGGAAGAAGC
Done.