Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013260.1 Corchorus capsularis cultivar CVL-1 contig13281, 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: 123542
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4472 original size:455 final size:454
Alignment explanation
Indices: 3614--4958 Score: 2298
Period size: 455 Copynumber: 3.0 Consensus size: 454
3604 ATGTATTATC
* * *
3614 TAGCCTTTCTGTAAGTATGAATTAACGAACATTGCCAATCACGCTGAAGCAAGTCTCGGCATCGC
1 TAGCCTCTCTGTAAGTATGAATTAACGAACACTGCCAATCACGCTGAAACAAGTCTCGGCATCGC
*
3679 TGCATAACTGGTGATAAATGATCGATCCTGTAAGGCTGGAAACTGTAGAATTTTATTTACAGCAA
66 TGCATAACTGGTGATAAATGATCGATCCTGTAAGGCTGGAAGCTGTAGAATTTTATTTACAGCAA
* *
3744 CCAGTGAATCCGATCCACAATGACCAGTCTATATCCATGTTCCCAAGCAAATGGCAGACCATGAT
131 CCAGTGAATCGGATCCACAATGACCAGTCTATATCCATGTTCCCAAGCAAGTGGCAGACCATGAT
* * * * *
3809 AAATGGCATACAATTTAGCCATCAAAATATGCCCCCACCAAACTTACAAGTAAATCTGAATAGCC
196 AAATGGCATACAATTCAGCCTTCGAAATATGCCCCCACCAAACTTACAAGTAAAGCCGAATAGCC
** *
3874 ACATACCAACTGAATCTACAAATGCCGCCAGCCGCAAGGTCACCGGGATTCGTTCTAGTAGCTGC
261 ACATACCAACTGAATCTACAAATGCCGCCAGCCGCAAGGTCA-TAGGATTCGTTCTAGCAGCTGC
** * *
3939 ATCAACATTAAGCTTGACAAACCTCGTAGAAGGCTTTACCCATCCAATAAGCGCAATAGTTCTGC
325 ATCAACATTAAGCTTGACAAACCTCGTAGAAGGCTTTACCCATCTGATAAGCGTAACAGTTCTGC
4004 GATTTGGAAGCTGTAAATTCAACCT-AAAGCTGCAAAACTCACAAACAAGTACTCTACACACATG
390 GATTTGGAAGCTGTAAATTCAACCTGAAA-CTGCAAAACTCACAAACAAGTACTCTACACACATG
4068 T
454 T
*
4069 TAGCCTCTCTGTAAGTATGAATTAACGAACACTGCCAATCACGCTGAAACAAGTCTCGGCATCGT
1 TAGCCTCTCTGTAAGTATGAATTAACGAACACTGCCAATCACGCTGAAACAAGTCTCGGCATCGC
* *
4134 TGCATAACTGGTGATAAATGATCTATCCTGTAAGGTTGGAAGCTGTAGAATTTTATTTACAGCAA
66 TGCATAACTGGTGATAAATGATCGATCCTGTAAGGCTGGAAGCTGTAGAATTTTATTTACAGCAA
*
4199 CCAGTGAATCGGATCCACAATGACCAGTCTATATCCATGTTTCCAAGCAAGTGGCAGACCATGAT
131 CCAGTGAATCGGATCCACAATGACCAGTCTATATCCATGTTCCCAAGCAAGTGGCAGACCATGAT
* *
4264 AAATGGCATACAATTCAGCCTTCGGAATATGCCCCCACCAAACTTACAAGTAAAGCCGAATAGCA
196 AAATGGCATACAATTCAGCCTTCGAAATATGCCCCCACCAAACTTACAAGTAAAGCCGAATAGCC
*
4329 ACATACCAACTGAATCTACAAATGCCGCCAGCCGCAAGGTCATTAGGATTCGTTCTAGCAACTGC
261 ACATACCAACTGAATCTACAAATGCCGCCAGCCGCAAGGTCA-TAGGATTCGTTCTAGCAGCTGC
*
4394 ATCAACATTAAGCTTGACAAACCTCGTAGAAGGCTTTACCCATCTGATAAGCGTAGCAGTTCTGC
325 ATCAACATTAAGCTTGACAAACCTCGTAGAAGGCTTTACCCATCTGATAAGCGTAACAGTTCTGC
*
4459 GATTTGGAAGCTGTAAATTCAACCTGAAACTGCAAAACTCACAAACAAGTAGTCTACACACATGT
390 GATTTGGAAGCTGTAAATTCAACCTGAAACTGCAAAACTCACAAACAAGTACTCTACACACATGT
* *
4524 TAGCCTCCCTGTAAGTATGAATTAACGAACACTGCCAATCACGCTGAAACAAGTCTCAGCATCGC
1 TAGCCTCTCTGTAAGTATGAATTAACGAACACTGCCAATCACGCTGAAACAAGTCTCGGCATCGC
*
4589 TGCATAACTGGTGATAAAGGATCGATCCTGTAAGGCTGGAAGCTGTAGAATTTTATTTACAGCAA
66 TGCATAACTGGTGATAAATGATCGATCCTGTAAGGCTGGAAGCTGTAGAATTTTATTTACAGCAA
* *
4654 CCAGTGAATCGGATCCACAATGATCAGTCTATATCCATGTTCCCAAGCAAGTGGCGGACCATGAT
131 CCAGTGAATCGGATCCACAATGACCAGTCTATATCCATGTTCCCAAGCAAGTGGCAGACCATGAT
* * *
4719 AAATGGCATATAATTCAGCCTTCGAAATATGCCCCCACCAAACTTACAAGTAAAGTCGAATAACC
196 AAATGGCATACAATTCAGCCTTCGAAATATGCCCCCACCAAACTTACAAGTAAAGCCGAATAGCC
4784 ACATACCAACTGAATCTACAAATGCCGCCAGCCGCAAGGTC-TAGGATTCGTTCTAGCAGCTGCA
261 ACATACCAACTGAATCTACAAATGCCGCCAGCCGCAAGGTCATAGGATTCGTTCTAGCAGCTGCA
* * *
4848 TCAACATTAAGCTTGACAAATCTCGTAGAAGGCTTTACCCATCTGATAAGCGTAACAGTTCTACT
326 TCAACATTAAGCTTGACAAACCTCGTAGAAGGCTTTACCCATCTGATAAGCGTAACAGTTCTGCG
*
4913 ATTTGGAAGTTGTAAATTCAACCTGAAACTGCAAAACTCACAAACA
391 ATTTGGAAGCTGTAAATTCAACCTGAAACTGCAAAACTCACAAACA
4959 CTAGAAAAGA
Statistics
Matches: 841, Mismatches: 48, Indels: 4
0.94 0.05 0.00
Matches are distributed among these distances:
453 128 0.15
455 710 0.84
456 3 0.00
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (454 bp):
TAGCCTCTCTGTAAGTATGAATTAACGAACACTGCCAATCACGCTGAAACAAGTCTCGGCATCGC
TGCATAACTGGTGATAAATGATCGATCCTGTAAGGCTGGAAGCTGTAGAATTTTATTTACAGCAA
CCAGTGAATCGGATCCACAATGACCAGTCTATATCCATGTTCCCAAGCAAGTGGCAGACCATGAT
AAATGGCATACAATTCAGCCTTCGAAATATGCCCCCACCAAACTTACAAGTAAAGCCGAATAGCC
ACATACCAACTGAATCTACAAATGCCGCCAGCCGCAAGGTCATAGGATTCGTTCTAGCAGCTGCA
TCAACATTAAGCTTGACAAACCTCGTAGAAGGCTTTACCCATCTGATAAGCGTAACAGTTCTGCG
ATTTGGAAGCTGTAAATTCAACCTGAAACTGCAAAACTCACAAACAAGTACTCTACACACATGT
Found at i:7160 original size:15 final size:15
Alignment explanation
Indices: 7115--7163 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
7105 CGTGTATATT
7115 ATATTATTAAATAAA
1 ATATTATTAAATAAA
*
7130 AT-TTCACTCAAA-AAA
1 ATATT-A-TTAAATAAA
7145 ATATTATTAAATAAA
1 ATATTATTAAATAAA
7160 ATAT
1 ATAT
7164 ATAATATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 6 0.21
15 16 0.57
16 6 0.21
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (15 bp):
ATATTATTAAATAAA
Found at i:16257 original size:159 final size:159
Alignment explanation
Indices: 15963--16258 Score: 461
Period size: 159 Copynumber: 1.9 Consensus size: 159
15953 TGAAAGGCCC
15963 CATGAACTTGAAGAGAATATGGGATGAACAACAAGCTGCAGAAAGCTTTTGCAATTTAGAAGATC
1 CATGAACTTGAAGAGAATATGGGATGAACAACAAGCTGCAGAAAGCTTTTGCAATTTAGAAGATC
***
16028 TTGTGGTCGAAAACTGCAAAAGTTTATTGAGTATTTTTCCATTCAATATGTTGGGAAGACTACAA
66 TTGTGGTCGAAAACTGCAAAAGTTTATTGAGTATTTTTCCATTCAATATGTCAAGAAGACTACAA
16093 AAGCTGAAAACTTTGAAAATAAGAGACCT
131 AAGCTGAAAACTTTGAAAATAAGAGACCT
* * *
16122 CATGGACTTGAAGAGAATATGGGATGAGCAACAAGCTGCAGATAGCTTTTGCAATTTAGAA-ATT
1 CATGAACTTGAAGAGAATATGGGATGAACAACAAGCTGCAGAAAGCTTTTGCAATTTAGAAGA-T
* * * * *
16186 CTTGTGGTTGAAGAGTGC-AAAGCTTTATTGAGTATTTTTCCATTCATTATGTCAAGAAGACTGC
65 CTTGTGGTCGAAAACTGCAAAAG-TTTATTGAGTATTTTTCCATTCAATATGTCAAGAAGACTAC
16250 AAAAGCTGA
129 AAAAGCTGA
16259 GACTATTGGG
Statistics
Matches: 124, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
158 5 0.04
159 119 0.96
ACGTcount: A:0.36, C:0.13, G:0.22, T:0.29
Consensus pattern (159 bp):
CATGAACTTGAAGAGAATATGGGATGAACAACAAGCTGCAGAAAGCTTTTGCAATTTAGAAGATC
TTGTGGTCGAAAACTGCAAAAGTTTATTGAGTATTTTTCCATTCAATATGTCAAGAAGACTACAA
AAGCTGAAAACTTTGAAAATAAGAGACCT
Found at i:19471 original size:11 final size:11
Alignment explanation
Indices: 19455--19480 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
19445 TCGGTTTTCC
19455 AAATATATTTT
1 AAATATATTTT
19466 AAATATATTTT
1 AAATATATTTT
19477 AAAT
1 AAAT
19481 TTTATTTATT
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:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
AAATATATTTT
Found at i:19948 original size:22 final size:22
Alignment explanation
Indices: 19923--19964 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
19913 AAGTTTTTAT
*
19923 TATTAAAACATATATATATATA
1 TATTAAAACATAAATATATATA
**
19945 TATTAATTCATAAATATATA
1 TATTAAAACATAAATATATA
19965 AATCAATAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (22 bp):
TATTAAAACATAAATATATATA
Found at i:23031 original size:25 final size:25
Alignment explanation
Indices: 23002--23051 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
22992 TTGTACTGTA
23002 GAAA-TTGAATTTTTCTAAATAAAAT
1 GAAATTTGAA-TTTTCTAAATAAAAT
23027 GAAATTTGAATTTTCTAAATAAAAT
1 GAAATTTGAATTTTCTAAATAAAAT
23052 ATTTTAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 19 0.79
26 5 0.21
ACGTcount: A:0.48, C:0.04, G:0.08, T:0.40
Consensus pattern (25 bp):
GAAATTTGAATTTTCTAAATAAAAT
Found at i:23323 original size:10 final size:10
Alignment explanation
Indices: 23297--23336 Score: 62
Period size: 10 Copynumber: 3.9 Consensus size: 10
23287 GTACTTTTAT
*
23297 ATATAGTATAT
1 ATATAG-ATAG
23308 ATATAGATAG
1 ATATAGATAG
23318 ATATAGATAG
1 ATATAGATAG
23328 ATATAGATA
1 ATATAGATA
23337 TATTTCTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
10 22 0.79
11 6 0.21
ACGTcount: A:0.50, C:0.00, G:0.15, T:0.35
Consensus pattern (10 bp):
ATATAGATAG
Found at i:34205 original size:26 final size:28
Alignment explanation
Indices: 34176--34252 Score: 86
Period size: 30 Copynumber: 2.7 Consensus size: 28
34166 CAATTTAATA
*
34176 TAAACAAATCAATAAACCTTT-T-CATT
1 TAAACAAATCAATAAACCTTTCTAAATT
*
34202 TAAACAAATCAATTAAACATTTCCTAAATT
1 TAAACAAATCAA-TAAACCTTT-CTAAATT
34232 TAAACAAATCTAATATAACCT
1 TAAACAAATC-AATA-AACCT
34253 CTACAATTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
26 12 0.29
27 8 0.19
29 1 0.02
30 15 0.36
31 6 0.14
ACGTcount: A:0.49, C:0.18, G:0.00, T:0.32
Consensus pattern (28 bp):
TAAACAAATCAATAAACCTTTCTAAATT
Found at i:34234 original size:30 final size:26
Alignment explanation
Indices: 34169--34246 Score: 84
Period size: 26 Copynumber: 2.8 Consensus size: 26
34159 CCTAAATCAA
* *
34169 TTTAATATAAACAAATCAATAAACCT
1 TTTAATTTAAACAAATCAATAAACAT
*
34195 TTTCATTTAAACAAATCAATTAAACAT
1 TTTAATTTAAACAAATCAA-TAAACAT
34222 TTCCTAAATTTAAACAAATCTAATA
1 TT--T-AATTTAAACAAATC-AATA
34247 TAACCTCTAC
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
26 17 0.40
27 8 0.19
29 1 0.02
30 15 0.35
31 2 0.05
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (26 bp):
TTTAATTTAAACAAATCAATAAACAT
Found at i:39706 original size:31 final size:30
Alignment explanation
Indices: 39668--39751 Score: 91
Period size: 29 Copynumber: 2.8 Consensus size: 30
39658 TTAATGCCCT
*
39668 TTTTGCCCCCTGAACTTGTATGATTTT-GACG
1 TTTTGCCCCCTGAACTTGTA--ATTTTGGACA
*
39699 TTTTGCCCCCTAAACTT-TAATTTTGGACA
1 TTTTGCCCCCTGAACTTGTAATTTTGGACA
* * *
39728 TTTTGTCCCTTGAACTTGCAATTT
1 TTTTGCCCCCTGAACTTGTAATTT
39752 GAAGCCATTT
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
28 5 0.11
29 17 0.38
30 7 0.16
31 16 0.36
ACGTcount: A:0.19, C:0.23, G:0.14, T:0.44
Consensus pattern (30 bp):
TTTTGCCCCCTGAACTTGTAATTTTGGACA
Found at i:43522 original size:81 final size:83
Alignment explanation
Indices: 43405--43559 Score: 224
Period size: 81 Copynumber: 1.9 Consensus size: 83
43395 AGAGAGAGAG
* * * * *
43405 AATTCTGTTGGATTAGATATAAAAAAAAGGCCCAAAGAGAAGAGAGAATGCCCAAATAAAAGAGG
1 AATTATGTTCGATTAGA-ATAAAAAAAAGGCCCAAAGAAAAGAGAGAAGGCCCAAATAAAAGAAG
*
43470 GGCCCAAAAAAAAGCTAAA
65 AGCCCAAAAAAAAGCTAAA
*
43489 AATTATGTTCGATTAG-ATAAAAAAAA-GCCCAAAGAAAAGAGAGAAGGCCTAAATAAAAGAAGA
1 AATTATGTTCGATTAGAATAAAAAAAAGGCCCAAAGAAAAGAGAGAAGGCCCAAATAAAAGAAGA
43552 GCCCAAAA
66 GCCCAAAA
43560 GAAACATTAT
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
81 40 0.62
82 10 0.16
84 14 0.22
ACGTcount: A:0.53, C:0.13, G:0.20, T:0.14
Consensus pattern (83 bp):
AATTATGTTCGATTAGAATAAAAAAAAGGCCCAAAGAAAAGAGAGAAGGCCCAAATAAAAGAAGA
GCCCAAAAAAAAGCTAAA
Found at i:56021 original size:11 final size:9
Alignment explanation
Indices: 55995--56019 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
55985 ATTAAAAATA
55995 ATATATAGT
1 ATATATAGT
56004 ATATATAGT
1 ATATATAGT
56013 ATATATA
1 ATATATA
56020 TACCCTTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (9 bp):
ATATATAGT
Found at i:71995 original size:15 final size:15
Alignment explanation
Indices: 71940--71994 Score: 65
Period size: 15 Copynumber: 3.7 Consensus size: 15
71930 ACCACGAAAT
71940 CCACCACCTCCACGA
1 CCACCACCTCCACGA
*
71955 CCACCACCTCCACGG
1 CCACCACCTCCACGA
** * *
71970 CCAAAACCTCTACCA
1 CCACCACCTCCACGA
71985 CCACCACCTC
1 CCACCACCTC
71995 TTCCGCCTCC
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.27, C:0.58, G:0.05, T:0.09
Consensus pattern (15 bp):
CCACCACCTCCACGA
Found at i:74693 original size:91 final size:92
Alignment explanation
Indices: 74531--74715 Score: 291
Period size: 91 Copynumber: 2.0 Consensus size: 92
74521 GTTCTGAGGC
* * * *
74531 CAACTTCAAAAACTGTTGAAAAAACTACTGAAGGAGGACTTGTTCTGAGGTCTATTGCTAAAGGC
1 CAACTTCAAAAACTGTTG-AAAAACTACTGAAGGAGGACCTGTTCTAAGGTCTACTACTAAAGGC
* * *
74596 GGCCTGCCATGATGTCAGATGGTATCCA
65 GACCTGCCATAATGTCAGATGATATCCA
74624 CAACTTCAAAAACTGTTG-AAAACTACTGAAGGAGGACCTGTTCTAAGGTCTACTACTAAAGGCG
1 CAACTTCAAAAACTGTTGAAAAACTACTGAAGGAGGACCTGTTCTAAGGTCTACTACTAAAGGCG
74688 ACCTGCCATAATGTCAGATGATATCCA
66 ACCTGCCATAATGTCAGATGATATCCA
74715 C
1 C
74716 GTCATTATGT
Statistics
Matches: 85, Mismatches: 7, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
91 67 0.79
93 18 0.21
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (92 bp):
CAACTTCAAAAACTGTTGAAAAACTACTGAAGGAGGACCTGTTCTAAGGTCTACTACTAAAGGCG
ACCTGCCATAATGTCAGATGATATCCA
Found at i:74730 original size:24 final size:25
Alignment explanation
Indices: 74698--74750 Score: 81
Period size: 24 Copynumber: 2.1 Consensus size: 25
74688 ACCTGCCATA
74698 ATGTCAGATGATATCCACGT-CATT
1 ATGTCAGATGATATCCACGTACATT
*
74722 ATGTCAGATGATATGCACGTGACATT
1 ATGTCAGATGATATCCACGT-ACATT
74748 ATG
1 ATG
74751 GATGATATGC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 19 0.73
26 7 0.27
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (25 bp):
ATGTCAGATGATATCCACGTACATT
Found at i:75822 original size:57 final size:57
Alignment explanation
Indices: 75756--75871 Score: 196
Period size: 57 Copynumber: 2.0 Consensus size: 57
75746 GCCAAAACCT
* *
75756 CTACCGCCACCTCTGCCACCCCCACGACCACCTCTTCCTCCTGCTTGTGCTTGTCCC
1 CTACCGCCACCTCTGCCACCCCCACGACCACCTCTTCCACCTGCTTGTGCCTGTCCC
* *
75813 CTACCGCCACCTCTGCCACCTCCACGACCACCTCTTCCACCTGGTTGTGCCTGTCCC
1 CTACCGCCACCTCTGCCACCCCCACGACCACCTCTTCCACCTGCTTGTGCCTGTCCC
75870 CT
1 CT
75872 GCAAATTATA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
57 55 1.00
ACGTcount: A:0.11, C:0.52, G:0.13, T:0.24
Consensus pattern (57 bp):
CTACCGCCACCTCTGCCACCCCCACGACCACCTCTTCCACCTGCTTGTGCCTGTCCC
Found at i:76766 original size:2 final size:2
Alignment explanation
Indices: 76759--76797 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
76749 AACCCTACCA
76759 AT AT AT AT AT AT 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 AT AT AT AT AT AT A
76798 ACTTCTATGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:77601 original size:64 final size:65
Alignment explanation
Indices: 77513--77639 Score: 220
Period size: 64 Copynumber: 2.0 Consensus size: 65
77503 AAATATTATA
* *
77513 TTTATCCTATAATGGGTAGTTTTTATTTTATTTTGAACTTTTAAAAAACTGAATTTGTCTCCGTT
1 TTTATCCTAAAATGGGTAGTTTTTATTTTATTTTGAAATTTTAAAAAACTGAATTTGTCTCCGTT
*
77578 TTTAT-CTAAAATGGGTAGTTTTTATTTTATTTTGAAATTTTAAAAAACTGAGTTTGTCTCCG
1 TTTATCCTAAAATGGGTAGTTTTTATTTTATTTTGAAATTTTAAAAAACTGAATTTGTCTCCG
77640 AGTCAACTCG
Statistics
Matches: 59, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
64 54 0.92
65 5 0.08
ACGTcount: A:0.28, C:0.09, G:0.13, T:0.50
Consensus pattern (65 bp):
TTTATCCTAAAATGGGTAGTTTTTATTTTATTTTGAAATTTTAAAAAACTGAATTTGTCTCCGTT
Found at i:77814 original size:15 final size:16
Alignment explanation
Indices: 77794--77836 Score: 79
Period size: 15 Copynumber: 2.8 Consensus size: 16
77784 ATTGGGCAGG
77794 TTCGGGTTCGGGTA-T
1 TTCGGGTTCGGGTATT
77809 TTCGGGTTCGGGTATT
1 TTCGGGTTCGGGTATT
77825 TTCGGGTTCGGG
1 TTCGGGTTCGGG
77837 CTCGGGTCGG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 14 0.52
16 13 0.48
ACGTcount: A:0.05, C:0.14, G:0.42, T:0.40
Consensus pattern (16 bp):
TTCGGGTTCGGGTATT
Found at i:78664 original size:16 final size:16
Alignment explanation
Indices: 78645--78686 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
78635 GGTTGTCTCG
* *
78645 GGTTTGGGTATTTTCA
1 GGTTCGGGTAATTTCA
*
78661 GGTTCGGGTAATTTCG
1 GGTTCGGGTAATTTCA
78677 GGTTCGGGTA
1 GGTTCGGGTA
78687 CAGGCGGGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.12, C:0.10, G:0.38, T:0.40
Consensus pattern (16 bp):
GGTTCGGGTAATTTCA
Found at i:90560 original size:144 final size:144
Alignment explanation
Indices: 90300--90588 Score: 533
Period size: 144 Copynumber: 2.0 Consensus size: 144
90290 AATAAACAAG
*
90300 AACTCTTATTAATTTGGGAGAAAACGATACAACACTTCAACAATACAAGATATAGACCCCTTATA
1 AACTCTTATTAATTTGGGAGAAAACGATACAACACTTCAACAATACAAGATATAGACCCATTATA
*
90365 TAAACATACGGTATTTCGCCTGTTTTTGCGTCTTCCCCGCATGAGGTCTGTGATGGAAGCGGAGG
66 TAAACATACGGTATTTCGCATGTTTTTGCGTCTTCCCCGCATGAGGTCTGTGATGGAAGCGGAGG
*
90430 GATCGGGTTGAAAA
131 GATCGGGTCGAAAA
* *
90444 AACTCTTATTAATTTGGGAGAAAATGATACAACACTTCAAGAATACAAGATATAGACCCATTATA
1 AACTCTTATTAATTTGGGAGAAAACGATACAACACTTCAACAATACAAGATATAGACCCATTATA
90509 TAAACATACGGTATTTCGCATGTTTTTGCGTCTTCCCCGCATGAGGTCTGTGATGGAAGCGGAGG
66 TAAACATACGGTATTTCGCATGTTTTTGCGTCTTCCCCGCATGAGGTCTGTGATGGAAGCGGAGG
90574 GATCGGGTCGAAAA
131 GATCGGGTCGAAAA
90588 A
1 A
90589 TCCACAAAAT
Statistics
Matches: 140, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
144 140 1.00
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (144 bp):
AACTCTTATTAATTTGGGAGAAAACGATACAACACTTCAACAATACAAGATATAGACCCATTATA
TAAACATACGGTATTTCGCATGTTTTTGCGTCTTCCCCGCATGAGGTCTGTGATGGAAGCGGAGG
GATCGGGTCGAAAA
Found at i:90634 original size:46 final size:46
Alignment explanation
Indices: 90557--90648 Score: 157
Period size: 46 Copynumber: 2.0 Consensus size: 46
90547 GCATGAGGTC
* * *
90557 TGTGATGGAAGCGGAGGGATCGGGTCGAAAAATCCACAAAATTCGT
1 TGTGATGGAAGCGGAGGGATCAGGCCAAAAAATCCACAAAATTCGT
90603 TGTGATGGAAGCGGAGGGATCAGGCCAAAAAATCCACAAAATTCGT
1 TGTGATGGAAGCGGAGGGATCAGGCCAAAAAATCCACAAAATTCGT
90649 AGCTCCACAA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.35, C:0.16, G:0.30, T:0.18
Consensus pattern (46 bp):
TGTGATGGAAGCGGAGGGATCAGGCCAAAAAATCCACAAAATTCGT
Found at i:92140 original size:21 final size:21
Alignment explanation
Indices: 92116--92159 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
92106 TTTATCTGGA
*
92116 TTGCTAAAT-ACCGCTCCATTT
1 TTGCT-AATCACCGCCCCATTT
*
92137 TTGCTATTCACCGCCCCATTT
1 TTGCTAATCACCGCCCCATTT
92158 TT
1 TT
92160 TACGCTTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.18, C:0.32, G:0.09, T:0.41
Consensus pattern (21 bp):
TTGCTAATCACCGCCCCATTT
Found at i:92402 original size:33 final size:33
Alignment explanation
Indices: 92360--92432 Score: 112
Period size: 33 Copynumber: 2.2 Consensus size: 33
92350 GCCGCCCCAG
*
92360 TGGGGAGGCTCCGCCGTGGTTGAGCC-TCCCTAA
1 TGGGGAGGCTCCGCCGTGGCTGAGCCGT-CCTAA
*
92393 TGGGGAGGCTCCGCCGTGGCTGAGCCGTCCTAG
1 TGGGGAGGCTCCGCCGTGGCTGAGCCGTCCTAA
92426 TGGGGAG
1 TGGGGAG
92433 ACTCAGTGTA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
33 36 0.97
34 1 0.03
ACGTcount: A:0.11, C:0.27, G:0.42, T:0.19
Consensus pattern (33 bp):
TGGGGAGGCTCCGCCGTGGCTGAGCCGTCCTAA
Found at i:93779 original size:2 final size:2
Alignment explanation
Indices: 93766--93801 Score: 63
Period size: 2 Copynumber: 17.5 Consensus size: 2
93756 TACTTTTTAG
93766 TA TA TCA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
93802 TAAAACTTAG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 31 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:93935 original size:22 final size:22
Alignment explanation
Indices: 93910--94039 Score: 152
Period size: 22 Copynumber: 5.5 Consensus size: 22
93900 TATCTAATTG
93910 ATTGATTAATTAAATTTATCTA
1 ATTGATTAATTAAATTTATCTA
93932 ATTGATTGATCAATTAAATTTATCTA
1 ATTGA-T--T-AATTAAATTTATCTA
*
93958 ATTGATTGATTAAATTTATCTA
1 ATTGATTAATTAAATTTATCTA
*
93980 ATTGATTGATCAATTAAATTTACCTA
1 ATTGA-T--T-AATTAAATTTATCTA
*
94006 ATTGATTGATTAAATTTATCTA
1 ATTGATTAATTAAATTTATCTA
*
94028 ATTGATTGATTA
1 ATTGATTAATTA
94040 TTTAAATTTA
Statistics
Matches: 95, Mismatches: 5, Indels: 16
0.82 0.04 0.14
Matches are distributed among these distances:
22 49 0.52
23 4 0.04
25 4 0.04
26 38 0.40
ACGTcount: A:0.38, C:0.06, G:0.08, T:0.48
Consensus pattern (22 bp):
ATTGATTAATTAAATTTATCTA
Found at i:93940 original size:30 final size:26
Alignment explanation
Indices: 93900--94055 Score: 213
Period size: 26 Copynumber: 6.3 Consensus size: 26
93890 GTCCAATTTG
*
93900 TATCTAATTGATTGATTAATTAAATT
1 TATCTAATTGATTGATCAATTAAATT
93926 TATCTAATTGATTGATCAATTAAATT
1 TATCTAATTGATTGATCAATTAAATT
93952 TATCTAATTGATTG----ATTAAATT
1 TATCTAATTGATTGATCAATTAAATT
93974 TATCTAATTGATTGATCAATTAAATT
1 TATCTAATTGATTGATCAATTAAATT
*
94000 TACCTAATTGATTG----ATTAAATT
1 TATCTAATTGATTGATCAATTAAATT
* *
94022 TATCTAATTGATTGATTATTTAAATT
1 TATCTAATTGATTGATCAATTAAATT
94048 TA-CTAATT
1 TATCTAATT
94056 ACAATATGCT
Statistics
Matches: 118, Mismatches: 4, Indels: 17
0.85 0.03 0.12
Matches are distributed among these distances:
22 43 0.36
25 6 0.05
26 69 0.58
ACGTcount: A:0.37, C:0.06, G:0.08, T:0.49
Consensus pattern (26 bp):
TATCTAATTGATTGATCAATTAAATT
Found at i:93977 original size:48 final size:47
Alignment explanation
Indices: 93910--94055 Score: 247
Period size: 48 Copynumber: 3.1 Consensus size: 47
93900 TATCTAATTG
*
93910 ATTGATTAATTAAATTTATCTAATTGATTGATCAATTAAATTTATCTA
1 ATTGATTGATTAAATTTATCTAATTGATTGATCAATTAAATTTA-CTA
93958 ATTGATTGATTAAATTTATCTAATTGATTGATCAATTAAATTTACCTA
1 ATTGATTGATTAAATTTATCTAATTGATTGATCAATTAAATTTA-CTA
* *
94006 ATTGATTGATTAAATTTATCTAATTGATTGATTATTTAAATTTACTA
1 ATTGATTGATTAAATTTATCTAATTGATTGATCAATTAAATTTACTA
94053 ATT
1 ATT
94056 ACAATATGCT
Statistics
Matches: 94, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
47 6 0.06
48 88 0.94
ACGTcount: A:0.38, C:0.06, G:0.08, T:0.49
Consensus pattern (47 bp):
ATTGATTGATTAAATTTATCTAATTGATTGATCAATTAAATTTACTA
Found at i:95783 original size:16 final size:16
Alignment explanation
Indices: 95762--95811 Score: 100
Period size: 16 Copynumber: 3.1 Consensus size: 16
95752 ACAATTCAGA
95762 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
95778 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
95794 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
95810 AA
1 AA
95812 ATATTTCAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.46, C:0.18, G:0.24, T:0.12
Consensus pattern (16 bp):
AAGCAGAAAAGCTCTG
Found at i:97936 original size:2 final size:2
Alignment explanation
Indices: 97929--97955 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
97919 CTTGCACAAT
97929 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
97956 TAATTGGCTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:99510 original size:22 final size:21
Alignment explanation
Indices: 99467--99507 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
99457 AACTGGATTG
99467 CTAAACACCGCCCCCCTTTTA
1 CTAAACACCGCCCCCCTTTTA
*
99488 CTAAATACCGCCCCCCTTTT
1 CTAAACACCGCCCCCCTTTT
99508 TACACTTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.22, C:0.46, G:0.05, T:0.27
Consensus pattern (21 bp):
CTAAACACCGCCCCCCTTTTA
Found at i:99607 original size:10 final size:10
Alignment explanation
Indices: 99594--99619 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
99584 CATTTCTAAC
99594 AACTTCTTCA
1 AACTTCTTCA
99604 AACTTCTTCA
1 AACTTCTTCA
99614 AACTTC
1 AACTTC
99620 ATTTCTAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.38
Consensus pattern (10 bp):
AACTTCTTCA
Found at i:99685 original size:26 final size:26
Alignment explanation
Indices: 99656--99723 Score: 109
Period size: 26 Copynumber: 2.6 Consensus size: 26
99646 TTTCTTCATT
99656 TTAATCATAAACTAATTAAATACTAA
1 TTAATCATAAACTAATTAAATACTAA
* *
99682 TTAATAATAAACTAATTAGATACTAA
1 TTAATCATAAACTAATTAAATACTAA
*
99708 TTAAACATAAACTAAT
1 TTAATCATAAACTAAT
99724 AAACTAAGTA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.54, C:0.10, G:0.01, T:0.34
Consensus pattern (26 bp):
TTAATCATAAACTAATTAAATACTAA
Found at i:99799 original size:19 final size:18
Alignment explanation
Indices: 99775--99811 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
99765 ACTAATTAAT
*
99775 ATTAAAAAATTTTAAAAAA
1 ATTAAAAAA-ATTAAAAAA
99794 ATTAAAAAAATTAAAAAA
1 ATTAAAAAAATTAAAAAA
99812 TGGTCGTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (18 bp):
ATTAAAAAAATTAAAAAA
Found at i:99810 original size:10 final size:9
Alignment explanation
Indices: 99775--99811 Score: 56
Period size: 9 Copynumber: 4.0 Consensus size: 9
99765 ACTAATTAAT
99775 ATTAAAAAA
1 ATTAAAAAA
*
99784 TTTTAAAAAA
1 -ATTAAAAAA
99794 ATTAAAAAA
1 ATTAAAAAA
99803 ATTAAAAAA
1 ATTAAAAAA
99812 TGGTCGTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
9 17 0.68
10 8 0.32
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (9 bp):
ATTAAAAAA
Found at i:100025 original size:21 final size:21
Alignment explanation
Indices: 99999--100039 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
99989 AAAAGGGGGG
**
99999 GGGGGGCGGTATTTAGCAAAA
1 GGGGGGCGGTAAATAGCAAAA
100020 GGGGGGCGGTAAATAGCAAA
1 GGGGGGCGGTAAATAGCAAA
100040 CCCCATAAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.32, C:0.10, G:0.44, T:0.15
Consensus pattern (21 bp):
GGGGGGCGGTAAATAGCAAAA
Found at i:102775 original size:37 final size:38
Alignment explanation
Indices: 102720--102798 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 38
102710 CTTATATACT
* *
102720 TGATCAACATACATGTCTTTTCATATAGACATAACTCTA
1 TGATCAACA-ACATGTCTTTCCAAATAGACATAACTCTA
*
102759 TGATCAAC-ACATGTCTTTCCAAATAGACATAACTTTA
1 TGATCAACAACATGTCTTTCCAAATAGACATAACTCTA
102796 TGA
1 TGA
102799 ATAATCATGT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 29 0.78
39 8 0.22
ACGTcount: A:0.37, C:0.20, G:0.09, T:0.34
Consensus pattern (38 bp):
TGATCAACAACATGTCTTTCCAAATAGACATAACTCTA
Found at i:105350 original size:37 final size:38
Alignment explanation
Indices: 105285--105363 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 38
105275 CTTCTATACT
* *
105285 TGATCAACATACATGTCTTTTCATATAGACATAACTTTA
1 TGATCAACA-ACATGTCTTTCCAAATAGACATAACTTTA
*
105324 TGATCAAC-ACATTTCTTTCCAAATAGACATAACTTTA
1 TGATCAACAACATGTCTTTCCAAATAGACATAACTTTA
105361 TGA
1 TGA
105364 ATAATCATGT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 29 0.78
39 8 0.22
ACGTcount: A:0.37, C:0.19, G:0.08, T:0.37
Consensus pattern (38 bp):
TGATCAACAACATGTCTTTCCAAATAGACATAACTTTA
Found at i:109808 original size:147 final size:145
Alignment explanation
Indices: 109533--110419 Score: 813
Period size: 147 Copynumber: 6.0 Consensus size: 145
109523 AACACTGAGA
* ** * *
109533 TCAAGGAATTCTAGATTCCTTAGAA-AAAACATTTCCGGAGGAATAGAACCATTGAACATATTTC
1 TCAAGGAATTCTAGATTCCTTA-AATGAAACAACTCCAGAGGAATAGAACCATTGAACACATTT-
* * * * * *
109597 TCCCCATGCCAAGATACACTAATTTTGTCAAATTGTTGAACCCTGTTCCTGGAATTTCACCTTGG
64 TCCCCATGTCAAGATGCACCAGTTTAGTCAAATTGCTGAACCCTG-TCCTGGAATTTCACCTTGG
* *
109662 ATTGAATTGTCGGAGATG
128 ATTGAATTGTAGGAAATG
* * *
109680 TCTAGGACTTCTAGATTCCTTAAATGAAACAACTCCAGAGGAATAGCACCATTGAACACATTATT
1 TCAAGGAATTCTAGATTCCTTAAATGAAACAACTCCAGAGGAATAGAACCATTGAACACATT-TT
* * *
109745 CCCCATGTAAAGACGCACTAGTTTAGTCAAATTGCTGAACCCTGTCCTAGGAATTTCACCTTGGA
65 CCCCATGTCAAGATGCACCAGTTTAGTCAAATTGCTGAACCCTGTCCT-GGAATTTCACCTTGGA
* * *
109810 GTAAATTGTGGGAAATG
129 TTGAATTGTAGGAAATG
* * * * **
109827 TCAAGGAATTCTAGATTCCTTAAATGAAACAATTCCAGGGGAATAGTACCATTGAAGA-AGTTGC
1 TCAAGGAATTCTAGATTCCTTAAATGAAACAACTCCAGAGGAATAGAACCATTGAACACA-TTTT
* * * * * * *
109891 CCCCAATGTCAAGTTCCACCAGTTCAGTCAAATTGCTTAACTCTGTCCCAGGAATTTCACCGCT-
65 CCCC-ATGTCAAGATGCACCAGTTTAGTCAAATTGCTGAACCCTGT-CCTGGAATTTCACC-TTG
*
109955 CATTGAATTGTAGGAAATG
127 GATTGAATTGTAGGAAATG
* * *** * **
109974 TCAAGGGATT-TCAGATTCCTTAAATGAAACAGCTGTGGAAGAATAGATTCATTGAAC-CAATTG
1 TCAAGGAATTCT-AGATTCCTTAAATGAAACAACTCCAGAGGAATAGAACCATTGAACAC-ATT-
* * * * * * * * *
110037 CTCCCCATGTCAAGGTGCACTAGTTCAGCCAAATTTCTGAACCCTGTCCCGGGGATTTCACCTTT
63 TTCCCCATGTCAAGATGCACCAGTTTAGTCAAATTGCTGAACCCTGT-CCTGGAATTTCACCTTG
** **
110102 GATAAAATTGCGGGAAATG
127 GATTGAATTGTAGGAAATG
* * *
110121 TCAAGGAATT-TCAGATTCCTTAAATGAAACAACTGCACAGGAATAAAACCATTG-A-ACATGTT
1 TCAAGGAATTCT-AGATTCCTTAAATGAAACAACTCCAGAGGAATAGAACCATTGAACACAT-TT
* * *
110183 TCGCCACATGCCAAGATGCACCAGTTTCGTCAAATTGCCGAACCCTGTCCCTGGAATTTCACCTT
64 TC-CC-CATGTCAAGATGCACCAGTTTAGTCAAATTGCTGAACCCTGT-CCTGGAATTTCACCTT
* *
110248 GGATTGAATTGAAAGAAATG
126 GGATTGAATTGTAGGAAATG
* * * * * * *
110268 TCAAGGAATTCTAGATTCCTTAGATGAAACAACTGCAAAGGAACAGAACCAGTGAATC-TATTGA
1 TCAAGGAATTCTAGATTCCTTAAATGAAACAACTCCAGAGGAATAGAACCATTGAA-CACATT-T
** * * *
110332 AACTCAAGTCAAGATGCACCAGTTTGGTCAAATTGCTGAACCCTGTCCTTGGAATTTCACCTTGG
64 TCCCCATGTCAAGATGCACCAGTTTAGTCAAATTGCTGAACCCTGTCC-TGGAATTTCACCTTGG
110397 ATT-AGATTGTAGGAAATG
128 ATTGA-ATTGTAGGAAATG
110415 TCAAG
1 TCAAG
110420 CAACGTCAGG
Statistics
Matches: 605, Mismatches: 112, Indels: 46
0.79 0.15 0.06
Matches are distributed among these distances:
145 4 0.01
146 21 0.03
147 565 0.93
148 13 0.02
149 2 0.00
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (145 bp):
TCAAGGAATTCTAGATTCCTTAAATGAAACAACTCCAGAGGAATAGAACCATTGAACACATTTTC
CCCATGTCAAGATGCACCAGTTTAGTCAAATTGCTGAACCCTGTCCTGGAATTTCACCTTGGATT
GAATTGTAGGAAATG
Found at i:110367 original size:441 final size:441
Alignment explanation
Indices: 109625--110419 Score: 991
Period size: 441 Copynumber: 1.8 Consensus size: 441
109615 CTAATTTTGT
* * ** * *
109625 CAAATTGTTGAACCCTGTTCCTGGAATTTCACCTTGGATTGAATTGTCGGAGATGTCTAGGACTT
1 CAAATTGTTGAACCCTGTCCCGGGAATTTCACCTTGGATAAAATTGTCGGAAATGTCAAGGACTT
* ** *
109690 CTAGATTCCTTAAATGAAACAACTCCAGAGGAATAGCACCATTGAACACATTATTCCCCATGTAA
66 CTAGATTCCTTAAATGAAACAACTCCACAGGAATAAAACCATTGAACACATTATTCCCCATGCAA
* * **
109755 AGACGCACTAGTTTAGTCAAATTGCTGAACCCTGTCCTAGGAATTTCACCTTGGAGTAAATTGTG
131 AGACGCACCAGTTTAGTCAAATTGCCGAACCCTGTCCTAGGAATTTCACCTTGGAGTAAATTGAA
* * ** * * * *
109820 GGAAATGTCAAGGAATTCTAGATTCCTTAAATGAAACAATTCCAGGGGAATAGTACCATTGAAGA
196 AGAAATGTCAAGGAATTCTAGATTCCTTAAATGAAACAACTCCAAAGGAACAGAACCAGTGAACA
** * * *
109885 AGTTGCCCCCAATGTCAAGTTCCACCAGTTCAGTCAAATTGCTTAACTCTGTCCCAGGAATTTCA
261 AGTTGAACCCAATGTCAAGATCCACCAGTTCAGTCAAATTGCTGAACCCTGTCCCAGGAATTTCA
109950 CCGCT-CATT-GAATTGTAGGAAATGTCAAGGGATTTCAGATTCCTTAAATGAAACAGCTGTGGA
326 CC-CTGCATTAG-ATTGTAGGAAATGTCAAGGGATTTCAGATTCCTTAAATGAAACAGCTGTGGA
110013 AGAATAGATTCATTGAACCAATTGCTCCCCATGTCAAGGTGCACTAGTTCAGC
389 AGAATAGATTCATTGAACCAATTGCTCCCCATGTCAAGGTGCACTAGTTCAGC
* * *
110066 CAAATT-TCTGAACCCTGTCCCGGGGATTTCACCTTTGATAAAATTG-CGGGAAATGTCAAGGAA
1 CAAATTGT-TGAACCCTGTCCCGGGAATTTCACCTTGGATAAAATTGTC-GGAAATGTCAAGGAC
*
110129 TT-TCAGATTCCTTAAATGAAACAACTGCACAGGAATAAAACCATTG-A-ACATGT-TTCGCCAC
64 TTCT-AGATTCCTTAAATGAAACAACTCCACAGGAATAAAACCATTGAACACAT-TATTC-CC-C
* * * * *
110190 ATGCCAAGATGCACCAGTTTCGTCAAATTGCCGAACCCTGTCCCT-GGAATTTCACCTTGGATTG
125 ATGCAAAGACGCACCAGTTTAGTCAAATTGCCGAACCCTGT-CCTAGGAATTTCACCTTGGAGTA
* *
110254 AATTGAAAGAAATGTCAAGGAATTCTAGATTCCTTAGATGAAACAACTGCAAAGGAACAGAACCA
189 AATTGAAAGAAATGTCAAGGAATTCTAGATTCCTTAAATGAAACAACTCCAAAGGAACAGAACCA
* * * ** **
110319 GTGAATCTA-TTGAAACTCAA-GTCAAGATGCACCAGTTTGGTCAAATTGCTGAACCCTGTCCTT
254 GTGAA-CAAGTTG-AACCCAATGTCAAGATCCACCAGTTCAGTCAAATTGCTGAACCCTGTCCCA
* *
110382 GGAATTTCACCTTGGATTAGATTGTAGGAAATGTCAAG
317 GGAATTTCACCCTGCATTAGATTGTAGGAAATGTCAAG
110420 CAACGTCAGG
Statistics
Matches: 296, Mismatches: 47, Indels: 22
0.81 0.13 0.06
Matches are distributed among these distances:
439 7 0.02
440 8 0.03
441 272 0.92
442 9 0.03
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (441 bp):
CAAATTGTTGAACCCTGTCCCGGGAATTTCACCTTGGATAAAATTGTCGGAAATGTCAAGGACTT
CTAGATTCCTTAAATGAAACAACTCCACAGGAATAAAACCATTGAACACATTATTCCCCATGCAA
AGACGCACCAGTTTAGTCAAATTGCCGAACCCTGTCCTAGGAATTTCACCTTGGAGTAAATTGAA
AGAAATGTCAAGGAATTCTAGATTCCTTAAATGAAACAACTCCAAAGGAACAGAACCAGTGAACA
AGTTGAACCCAATGTCAAGATCCACCAGTTCAGTCAAATTGCTGAACCCTGTCCCAGGAATTTCA
CCCTGCATTAGATTGTAGGAAATGTCAAGGGATTTCAGATTCCTTAAATGAAACAGCTGTGGAAG
AATAGATTCATTGAACCAATTGCTCCCCATGTCAAGGTGCACTAGTTCAGC
Found at i:118084 original size:154 final size:154
Alignment explanation
Indices: 117846--118313 Score: 868
Period size: 154 Copynumber: 3.0 Consensus size: 154
117836 ATGGTTTATC
117846 AACATATATACATGGATGTCTCTTAAAAATCATCCAAAAAAAACCTTTAAATAAGGATTTTTTGG
1 AACATATATACATGGATGTCTCTTAAAAATCATCCAAAAAAAACCTTTAAATAAGGATTTTTTGG
117911 GTTTTTTTTTATTATATTTTCCAATAAATAATTTTTTTTTACAAATATAAATTCACCCTTTAGAA
66 GTTTTTTTTTATTATATTTTCCAATAAATAATTTTTTTTTACAAATATAAATTCACCCTTTAGAA
117976 TTGTGTTTTTTTTTTACAAATATA
131 TTGTGTTTTTTTTTTACAAATATA
118000 AACATATATACATGGATGTCTCTTAAAAATCATCCAAAAAAAACCTTTAAATAAGGATTTTTTGG
1 AACATATATACATGGATGTCTCTTAAAAATCATCCAAAAAAAACCTTTAAATAAGGATTTTTTGG
118065 GTTTTTTTTTATTATATTTTCCAATAAATAATTTTTTTTTACAAATATAAATTCACCCTTTAGAA
66 GTTTTTTTTTATTATATTTTCCAATAAATAATTTTTTTTTACAAATATAAATTCACCCTTTAGAA
118130 TTGTGTTTTTTTTTTACAAATATA
131 TTGTGTTTTTTTTTTACAAATATA
118154 AACATATATACATGGATGTCTCTTAAAAAGTCATCCAAAAAAAACCTTTAAATAAGGATTTTTTT
1 AACATATATACATGGATGTCTCTTAAAAA-TCATCCAAAAAAAACCTTTAAATAAGGA-TTTTTT
118219 GGG--TTTTTTTATTATATTTTCCAATAAATAATATTTTTTTTTACAAATATAAATTCACCCTTT
64 GGGTTTTTTTTTATTATATTTTCCAATAAAT-A-ATTTTTTTTTACAAATATAAATTCACCCTTT
118282 AGAATTGTGTTTTTTTTTTTTACAAATATA
127 AGAATTGTG--TTTTTTTTTTACAAATATA
118312 AA
1 AA
118314 TTCACCCTTT
Statistics
Matches: 308, Mismatches: 0, Indels: 8
0.97 0.00 0.03
Matches are distributed among these distances:
154 209 0.68
155 29 0.09
156 49 0.16
158 21 0.07
ACGTcount: A:0.37, C:0.11, G:0.07, T:0.45
Consensus pattern (154 bp):
AACATATATACATGGATGTCTCTTAAAAATCATCCAAAAAAAACCTTTAAATAAGGATTTTTTGG
GTTTTTTTTTATTATATTTTCCAATAAATAATTTTTTTTTACAAATATAAATTCACCCTTTAGAA
TTGTGTTTTTTTTTTACAAATATA
Found at i:118298 original size:42 final size:42
Alignment explanation
Indices: 118252--118333 Score: 155
Period size: 42 Copynumber: 2.0 Consensus size: 42
118242 ATAAATAATA
118252 TTTTTTTTTACAAATATAAATTCACCCTTTAGAATTGTGTTT
1 TTTTTTTTTACAAATATAAATTCACCCTTTAGAATTGTGTTT
*
118294 TTTTTTTTTACAAATATAAATTCACCCTTTGGAATTGTGT
1 TTTTTTTTTACAAATATAAATTCACCCTTTAGAATTGTGT
118334 GCATGGAAAG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.28, C:0.12, G:0.09, T:0.51
Consensus pattern (42 bp):
TTTTTTTTTACAAATATAAATTCACCCTTTAGAATTGTGTTT
Found at i:123542 original size:1 final size:1
Alignment explanation
Indices: 123509--123534 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
123499 CAGCTCTAAC
123509 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
123535 TTCAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Done.