Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019189.1 Corchorus olitorius cultivar O-4 contig19222, 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: 75695
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:1550 original size:32 final size:32
Alignment explanation
Indices: 1481--1552 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 32
1471 CAAATTGATA
* * * * *
1481 GACAAAGTAGCCCTCGAATTTTGACATAGAAG
1 GACAAAATAACCCTCAAAATTTGACAAAGAAG
* *
1513 AACAAAATAACCCTCAAAATTTGACAAAGTAG
1 GACAAAATAACCCTCAAAATTTGACAAAGAAG
1545 GACAAAAT
1 GACAAAAT
1553 GTTCTTTGAA
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.47, C:0.18, G:0.15, T:0.19
Consensus pattern (32 bp):
GACAAAATAACCCTCAAAATTTGACAAAGAAG
Found at i:3007 original size:28 final size:29
Alignment explanation
Indices: 2973--3043 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
2963 ACTTGAAGCA
* *
2973 TTTGGACGTTTTGTC-CATGAACTTTAAT
1 TTTGGACGTTTTGTCTCATAAACTTCAAT
* * *
3001 TTTGGACATTTTATCTCCTAAACTTCAAT
1 TTTGGACGTTTTGTCTCATAAACTTCAAT
3030 TTTGAGACGTTTTG
1 TTTG-GACGTTTTG
3044 CCCCCTCAGG
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
28 13 0.38
29 14 0.41
30 7 0.21
ACGTcount: A:0.23, C:0.15, G:0.15, T:0.46
Consensus pattern (29 bp):
TTTGGACGTTTTGTCTCATAAACTTCAAT
Found at i:3292 original size:29 final size:29
Alignment explanation
Indices: 3223--3292 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 29
3213 TTGATGATGC
3223 CAAAACGTTCCAAAATTGAAATTCAAGGGA
1 CAAAACG-TCCAAAATTGAAATTCAAGGGA
* ** * *
3253 TAAAATATCCAAAATTGAAGTTTAATGGG-
1 CAAAACGTCCAAAATTGAAATTCAA-GGGA
3282 CAAAACGTCCA
1 CAAAACGTCCA
3293 TTTTACCCAA
Statistics
Matches: 31, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
29 24 0.77
30 7 0.23
ACGTcount: A:0.46, C:0.16, G:0.16, T:0.23
Consensus pattern (29 bp):
CAAAACGTCCAAAATTGAAATTCAAGGGA
Found at i:11498 original size:33 final size:33
Alignment explanation
Indices: 11453--11515 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
11443 TTCATGGTCG
* *
11453 AAAGAGATTTCAAAACCTATGGCTTGAGAATCA
1 AAAGAGAATTCAAAACCTATGGCTTAAGAATCA
11486 AAAGAGAATTCAAAACCTATGGCTTAAGAA
1 AAAGAGAATTCAAAACCTATGGCTTAAGAA
11516 AAAATTTCTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.46, C:0.14, G:0.17, T:0.22
Consensus pattern (33 bp):
AAAGAGAATTCAAAACCTATGGCTTAAGAATCA
Found at i:16852 original size:24 final size:24
Alignment explanation
Indices: 16802--16854 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
16792 GTCCCCGCCC
* *
16802 TCTTCTTCTTCCTCATCGTCTTCA
1 TCTTCTTCTTCCTCATCATCCTCA
*
16826 TCTTCTTCTTCTTCATCATCACT-A
1 TCTTCTTCTTCCTCATCATC-CTCA
16850 TCTTC
1 TCTTC
16855 CTCTAATTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 24 0.96
25 1 0.04
ACGTcount: A:0.11, C:0.36, G:0.02, T:0.51
Consensus pattern (24 bp):
TCTTCTTCTTCCTCATCATCCTCA
Found at i:16902 original size:30 final size:30
Alignment explanation
Indices: 16868--16932 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 30
16858 TAATTCTTCT
* *
16868 TCTTCTTCGACGTCCTCCTCCTCCTCGTCG
1 TCTTCCTCGACCTCCTCCTCCTCCTCGTCG
** * *
16898 TCTTCCTCTTCCTCCTCCTCCTCTTCTTCG
1 TCTTCCTCGACCTCCTCCTCCTCCTCGTCG
16928 TCTTC
1 TCTTC
16933 AGTATCTTCC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.02, C:0.48, G:0.08, T:0.43
Consensus pattern (30 bp):
TCTTCCTCGACCTCCTCCTCCTCCTCGTCG
Found at i:16910 original size:21 final size:21
Alignment explanation
Indices: 16880--16923 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
16870 TTCTTCGACG
* *
16880 TCCTCCTCCTCCTCGTCGTCT
1 TCCTCCTCCTCCTCCTCCTCT
*
16901 TCCTCTTCCTCCTCCTCCTCT
1 TCCTCCTCCTCCTCCTCCTCT
16922 TC
1 TC
16924 TTCGTCTTCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.00, C:0.55, G:0.05, T:0.41
Consensus pattern (21 bp):
TCCTCCTCCTCCTCCTCCTCT
Found at i:16915 original size:24 final size:24
Alignment explanation
Indices: 16883--16932 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
16873 TTCGACGTCC
*
16883 TCCTCCTCCTCGTCGTCTTCCTCT
1 TCCTCCTCCTCCTCGTCTTCCTCT
* *
16907 TCCTCCTCCTCCTCTTCTTCGTCT
1 TCCTCCTCCTCCTCGTCTTCCTCT
16931 TC
1 TC
16933 AGTATCTTCC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.00, C:0.50, G:0.06, T:0.44
Consensus pattern (24 bp):
TCCTCCTCCTCCTCGTCTTCCTCT
Found at i:17708 original size:135 final size:131
Alignment explanation
Indices: 17466--17735 Score: 398
Period size: 135 Copynumber: 2.0 Consensus size: 131
17456 AAAAATCTTC
* * *
17466 TTCTATTTTTCTACGCATGAACATGATATTTAACCGGTTGGTGATAGGAGGTAGCTCTCACCTAT
1 TTCTATTTTGCTACGCATGAACATGATATTTAACCGGTTGATAATAGGAGGTAGCTCTCACCTAT
* * *
17531 CCCGCGAATCCCACCCATACATCCTAGGATTCAAACTCGAGACCTCTCATAAAATATCCCAAATT
66 CCCGCAAATCCCACCCATACATCCTAGGATTCAAACTCGAGACCTCTCACAAAAAATCCCAAATT
17596 T
131 T
*
17597 TTCTATTTTGCTACTCATGAACATGATATTTAACCGGTTGATTATACAATAGGAGGTAGCTCTCA
1 TTCTATTTTGCTACGCATGAACATGATATTTAACCGGTTG---AT--AATAGGAGGTAGCTCTCA
* * *
17662 -CTATCTCGCAAATCCCACCCATACATCCTAGGATTCAAACTGGAGACCTTTCACAAAAAATCCC
61 CCTATCCCGCAAATCCCACCCATACATCCTAGGATTCAAACTCGAGACCTCTCACAAAAAATCCC
17726 AAATTT
126 AAATTT
17732 TTCT
1 TTCT
17736 CTCCATAAAA
Statistics
Matches: 124, Mismatches: 10, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
131 38 0.31
134 1 0.01
135 68 0.55
136 17 0.14
ACGTcount: A:0.30, C:0.26, G:0.13, T:0.31
Consensus pattern (131 bp):
TTCTATTTTGCTACGCATGAACATGATATTTAACCGGTTGATAATAGGAGGTAGCTCTCACCTAT
CCCGCAAATCCCACCCATACATCCTAGGATTCAAACTCGAGACCTCTCACAAAAAATCCCAAATT
T
Found at i:25955 original size:16 final size:16
Alignment explanation
Indices: 25934--25967 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
25924 AAGTGATGGA
*
25934 AGAAAATGAGATAGAG
1 AGAAAATGAGAGAGAG
*
25950 AGAAAATTAGAGAGAG
1 AGAAAATGAGAGAGAG
25966 AG
1 AG
25968 GCCCCATATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.32, T:0.12
Consensus pattern (16 bp):
AGAAAATGAGAGAGAG
Found at i:28863 original size:12 final size:12
Alignment explanation
Indices: 28846--28872 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
28836 CATTTTTTCC
28846 TTTTTTAATCTT
1 TTTTTTAATCTT
28858 TTTTTTAATCTT
1 TTTTTTAATCTT
28870 TTT
1 TTT
28873 CTTTTTCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTTTTAATCTT
Found at i:29938 original size:28 final size:28
Alignment explanation
Indices: 29873--29930 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
29863 TGCGTTTGTA
29873 ATCCCAATCTCTTCAAGAAATAAAAATG
1 ATCCCAATCTCTTCAAGAAATAAAAATG
29901 ATCCCAATCTCTTCAAGAAATAAAAATG
1 ATCCCAATCTCTTCAAGAAATAAAAATG
29929 AT
1 AT
29931 TCTTATCTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.47, C:0.21, G:0.07, T:0.26
Consensus pattern (28 bp):
ATCCCAATCTCTTCAAGAAATAAAAATG
Found at i:35669 original size:34 final size:34
Alignment explanation
Indices: 35631--35698 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
35621 ATTCTGAAAA
*
35631 GTCTGCAGGTGAAAGTCCGATGGGTCTGTAAATC
1 GTCTGCAGGTGAAAGTCCGATGGGTCCGTAAATC
35665 GTCTGCAGGTGAAAGTCCGATGGGTCCGTAAATC
1 GTCTGCAGGTGAAAGTCCGATGGGTCCGTAAATC
35699 CCAAAAATGG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (34 bp):
GTCTGCAGGTGAAAGTCCGATGGGTCCGTAAATC
Found at i:41205 original size:58 final size:58
Alignment explanation
Indices: 41110--41226 Score: 198
Period size: 58 Copynumber: 2.0 Consensus size: 58
41100 ACGATTTGGC
* * *
41110 ACCAGATATCCGGAGGTGTGGAAAGGGCTGTTATGAAAAGTGAAAAAACCATAAAAAA
1 ACCAGATATCCGGAGGTGTGGAAAGAGCTGCTATGAAAAATGAAAAAACCATAAAAAA
*
41168 ACCAGATATCCGGAGGTGTGGAAAGAGCTGCTGTGAAAAATGAAAAAACCATAAAAAA
1 ACCAGATATCCGGAGGTGTGGAAAGAGCTGCTATGAAAAATGAAAAAACCATAAAAAA
41226 A
1 A
41227 AAGTTTATTT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
58 55 1.00
ACGTcount: A:0.46, C:0.13, G:0.25, T:0.16
Consensus pattern (58 bp):
ACCAGATATCCGGAGGTGTGGAAAGAGCTGCTATGAAAAATGAAAAAACCATAAAAAA
Found at i:42643 original size:666 final size:668
Alignment explanation
Indices: 41251--43032 Score: 2882
Period size: 666 Copynumber: 2.7 Consensus size: 668
41241 AAGTTTTTTT
* * *
41251 GAAGCGTAAAAAGCCCTTTAA-TATTTTTGGCATTGAATTATAT-A-TTTTTGTGAGTATTGTGG
1 GAAGCGTGAAAA-CCCTTCAATTA-TTTTGGCATTGAATTATATAATTTTTTATGAGTATTGTGG
*
41313 CAAAAAATGGAG-GAAAGAA-TTTTCGGGTCAGTTTTTTCAAAAATTTTAGCCGAAATCGTGTAC
64 CAAAAAATTGAGTGAAA-AACTTTT-GGGTCAGTTTTTTCAAAAATTTTAGCCGAAATCGTGTAC
41376 TAACCATCATGATTTTTGGCTAAAAATGCGCTATGGGACCCCGGCTCAGTTTTGCATGATTTTTG
127 TAACCATCATGATTTTTGGCTAAAAATGCGCTATGGG-CCCCGGCTCAGTTTTGCATGATTTTTG
*
41441 GTGCCAAGACTCCTTGAAATATCTTTATTCATCTAACCAAATCTCAGCCGCAATGGGTTTAAGGA
191 GTGCCAAGACTCCTTGAAATATCTTTATTCATCTAACCAAATCTTAGCCGCAATGGGTTTAAGGA
*
41506 TTTGTTTTTGCGAGCATCTGAATCATGTTTCGATTTAGTTAAAAATTAATTTGG-AAAAATTTTG
256 TTTGTTTTTGCGAGCATCTGAATCATGTTTCGATTTAGTTAGAAATTAATTTGGAAAAAATTTTG
*
41570 AAAAACGATATTAGAAGCGTGAAAAGCCCTTCAATCTTGTTGGCATTGAATTATATATTTTTTGT
321 AAAAACGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCATTGAATTATATATTTTTTGT
41635 GAGTATTGTGGCAAAAAATGGAGG-AAAAATTTTCGGGTCAGTTTTTTCAAAAATTTTAGCCGAA
386 GAGTATTGTGGCAAAAAATGGAGGAAAAAATTTTCGGGTCAGTTTTTTCAAAAATTTTAGCCGAA
* * *
41699 ATCGTGTACTAACCATCATGATTTTTGGCTAAAAATGCGCTATGGGGCCCCGGCTCAGTTTTGCA
451 ATCGTGTACTAACCATCATGATTTTTGGCTAAAAATGCACTATGGGGCCCCGACTAAGTTTTGCA
* *
41764 TGATTTTTGGTGCCAAGACTCCTTGAAATATCTTTATTCATCTAACCAATCTTCAGCCGTAATGG
516 TGATTTTTGGTGCCAAGACTCCTTGAAATATCTTTATTCATCTAACCAATCTCCAGCCGCAATGG
*
41829 ATTTAAGGATTTGTTTTTGTCGAGCATCTGAATCATGTTTCGATTTAGTTAGAAATTAATTTGGA
581 ATTTAAGGAATTGTTTTTGTCGAGCATCTGAATCATGTTTCGATTTAGTTAGAAATTAATTTGGA
41894 AAAAATTTTGAAAGACGATATTA
646 AAAAATTTTGAAAGACGATATTA
* *
41917 GAAGCGTGAAAACCCTTCAATTATTTTGGTATTGAATTATATAATTTTTTATGTGTATTGTGGCA
1 GAAGCGTGAAAACCCTTCAATTATTTTGGCATTGAATTATATAATTTTTTATGAGTATTGTGGCA
* ** *
41982 AAAAATTGAGTGAAAAACTTTTGGGTCAG-TTTTTCAAAAATTTTGGTTGAAATCGTGTATTAAC
66 AAAAATTGAGTGAAAAACTTTTGGGTCAGTTTTTTCAAAAATTTTAGCCGAAATCGTGTACTAAC
* * * *
42046 CATCATGATTTTTGGCTAAAAATGCGCTATGGGCCCCGGCTCAATTTTGCATAATTTTTAGTGCG
131 CATCATGATTTTTGGCTAAAAATGCGCTATGGGCCCCGGCTCAGTTTTGCATGATTTTTGGTGCC
42111 AAGACTCCTTGAAATATCTTTATTCATCTAACCAAATCTTAGCCGCAATGGGTTTTAAGGATTTG
196 AAGACTCCTTGAAATATCTTTATTCATCTAACCAAATCTTAGCCGCAATGGG-TTTAAGGATTTG
* *
42176 TTTTTTGCGAGCATCTGAATCATGTTTCGATTTACTTAGAAATTAATTTGGAAAAAATCTTGAAA
260 -TTTTTGCGAGCATCTGAATCATGTTTCGATTTAGTTAGAAATTAATTTGGAAAAAATTTTGAAA
*
42241 AACGATATTAGAAGCGTGAAATGCCCTTCAATCTTTTTGGCATTGAATTATATATTTTTTGTGAG
324 AACGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCATTGAATTATATATTTTTTGTGAG
42306 TATTGTGGCAAAAAATGGAGGAAAAAATTTTCGGGTCAGTTTTTTCAAAAATTTTAGCCGAAATC
389 TATTGTGGCAAAAAATGGAGGAAAAAATTTTCGGGTCAGTTTTTTCAAAAATTTTAGCCGAAATC
*
42371 GTGTACTAACCATCATGATTTTTGGCTAAAAATGCACTATGGTGCCCCGACTAAGTTTTGCATGA
454 GTGTACTAACCATCATGATTTTTGGCTAAAAATGCACTATGGGGCCCCGACTAAGTTTTGCATGA
42436 TTTTTGGTGCCGAA-ACTCCTTGAAATATCTTTATTCATCTAACCAAATC-CCAGCCGCAATGGA
519 TTTTTGGTGCC-AAGACTCCTTGAAATATCTTTATTCATCTAACC-AATCTCCAGCCGCAATGGA
*
42499 TTTAAGGAATTGTTTTTG-CGAGTATCTGAATCATG-TTCGATTTAGTTAGAAATTAATTTGG-A
582 TTTAAGGAATTGTTTTTGTCGAGCATCTGAATCATGTTTCGATTTAGTTAGAAATTAATTTGGAA
42561 AAAATTTTGAAAGACGATATTA
647 AAAATTTTGAAAGACGATATTA
42583 GAAGCGTGAAAACCCTTCAATTATTTTGGCATTGAATTATATAATTTTTTATGAGTATTGTGGCA
1 GAAGCGTGAAAACCCTTCAATTATTTTGGCATTGAATTATATAATTTTTTATGAGTATTGTGGCA
* * * *
42648 AAAGATTGAGTAAAAAACTTTCGGGTCAGTTTTTTCAAAAATTTTCGCCGAAATCGTGTACT-A-
66 AAAAATTGAGTGAAAAACTTTTGGGTCAGTTTTTTCAAAAATTTTAGCCGAAATCGTGTACTAAC
*
42711 CATCATGATTTTTGGCTAAAAATGCGCTATGGGGCCCCGACTCAGTTTTGCATGATTTTTGGTGC
131 CATCATGATTTTTGGCTAAAAATGCGCTAT-GGGCCCCGGCTCAGTTTTGCATGATTTTTGGTGC
* * *
42776 TAAGACTCCTTGAAATATCTTTATTCATTTAATCAAAT-TTCAGCCGCAATGGGTTTAAGGATTT
195 CAAGACTCCTTGAAATATCTTTATTCATCTAACCAAATCTT-AGCCGCAATGGGTTTAAGGATTT
* *
42840 GTTTTTGCGAACGTCTGAATCATGTTTCGATTTAGTTAGAAATTAATTTGGAAAAAATTTTGAAA
259 GTTTTTGCGAGCATCTGAATCATGTTTCGATTTAGTTAGAAATTAATTTGGAAAAAATTTTGAAA
* * ** * *
42905 AACGATATTAAAAGCGCGAAAAAAAACCTTCAATCTTTCTT-GCGTTGAATCATATA--TTTTGT
324 AACGATATTAGAAGCGTG--AAAAGCCCTTCAATCTTT-TTGGCATTGAATTATATATTTTTTGT
* *
42967 GAGTATTGTGGCAAAAAATGGAGGAAAAAATTTTTGGGTCCGTTTTTTTCAAAAATTTTAGCCGA
386 GAGTATTGTGGCAAAAAATGGAGGAAAAAATTTTCGGGTCAG-TTTTTTCAAAAATTTTAGCCGA
43032 A
450 A
43033 GCCCGAAATC
Statistics
Matches: 1041, Mismatches: 57, Indels: 37
0.92 0.05 0.03
Matches are distributed among these distances:
664 122 0.12
665 171 0.16
666 308 0.30
667 140 0.13
668 120 0.12
669 174 0.17
670 6 0.01
ACGTcount: A:0.31, C:0.14, G:0.19, T:0.36
Consensus pattern (668 bp):
GAAGCGTGAAAACCCTTCAATTATTTTGGCATTGAATTATATAATTTTTTATGAGTATTGTGGCA
AAAAATTGAGTGAAAAACTTTTGGGTCAGTTTTTTCAAAAATTTTAGCCGAAATCGTGTACTAAC
CATCATGATTTTTGGCTAAAAATGCGCTATGGGCCCCGGCTCAGTTTTGCATGATTTTTGGTGCC
AAGACTCCTTGAAATATCTTTATTCATCTAACCAAATCTTAGCCGCAATGGGTTTAAGGATTTGT
TTTTGCGAGCATCTGAATCATGTTTCGATTTAGTTAGAAATTAATTTGGAAAAAATTTTGAAAAA
CGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCATTGAATTATATATTTTTTGTGAGTA
TTGTGGCAAAAAATGGAGGAAAAAATTTTCGGGTCAGTTTTTTCAAAAATTTTAGCCGAAATCGT
GTACTAACCATCATGATTTTTGGCTAAAAATGCACTATGGGGCCCCGACTAAGTTTTGCATGATT
TTTGGTGCCAAGACTCCTTGAAATATCTTTATTCATCTAACCAATCTCCAGCCGCAATGGATTTA
AGGAATTGTTTTTGTCGAGCATCTGAATCATGTTTCGATTTAGTTAGAAATTAATTTGGAAAAAA
TTTTGAAAGACGATATTA
Found at i:42692 original size:332 final size:332
Alignment explanation
Indices: 41251--43133 Score: 2774
Period size: 332 Copynumber: 5.6 Consensus size: 332
41241 AAGTTTTTTT
* * *
41251 GAAGCGTAAAAAGCCCTTTAATATTTTTGGCATTGAATTATATA-TTTTTGTGAGTATTGTGGCA
1 GAAGCGTGAAAA-CCCTTCAATCTTTTTGGCATTGAATTATATATTTTTTGTGAGTATTGTGGCA
*
41315 AAAAATGGAGGAAAGAATTTTCGGGTCAGTTTTTTCAAAAATTTTAGCCGAAATCGTGTACTAAC
65 AAAAATGGAGGAAAAAATTTTCGGGTCAGTTTTTTCAAAAATTTTAGCCGAAATCGTGTACTAAC
41380 CATCATGATTTTTGGCTAAAAATGCGCTATGGGACCCCGGCTCAGTTTTGCATGATTTTTGGTGC
130 CATCATGATTTTTGGCTAAAAATGCGCTATGGG-CCCCGGCTCAGTTTTGCATGATTTTTGGTGC
*
41445 CAAGACTCCTTGAAATATCTTTATTCATCTAACCAAATCTCAGCCGCAATGGGTTTAAGGATTTG
194 CAAGACTCCTTGAAATATCTTTATTCATCTAACCAAATCTCAGCCGCAATGGATTTAAGGATTTG
*
41510 TTTTTGCGAGCATCTGAATCATGTTTCGATTTAGTTAAAAATTAATTTGG-AAAAATTTTGAAAA
259 TTTTTGCGAGCATCTGAATCATGTTTCGATTTAGTTAGAAATTAATTTGGAAAAAATTTTGAAAA
41574 ACGATATTA
324 ACGATATTA
*
41583 GAAGCGTGAAAAGCCCTTCAATCTTGTTGGCATTGAATTATATATTTTTTGTGAGTATTGTGGCA
1 GAAGCGTGAAAA-CCCTTCAATCTTTTTGGCATTGAATTATATATTTTTTGTGAGTATTGTGGCA
41648 AAAAATGGAGG-AAAAATTTTCGGGTCAGTTTTTTCAAAAATTTTAGCCGAAATCGTGTACTAAC
65 AAAAATGGAGGAAAAAATTTTCGGGTCAGTTTTTTCAAAAATTTTAGCCGAAATCGTGTACTAAC
41712 CATCATGATTTTTGGCTAAAAATGCGCTATGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGTGC
130 CATCATGATTTTTGGCTAAAAATGCGCTAT-GGGCCCCGGCTCAGTTTTGCATGATTTTTGGTGC
*
41777 CAAGACTCCTTGAAATATCTTTATTCATCTAACC-AATCTTCAGCCGTAATGGATTTAAGGATTT
194 CAAGACTCCTTGAAATATCTTTATTCATCTAACCAAATC-TCAGCCGCAATGGATTTAAGGATTT
41841 GTTTTTGTCGAGCATCTGAATCATGTTTCGATTTAGTTAGAAATTAATTTGGAAAAAATTTTGAA
258 GTTTTTG-CGAGCATCTGAATCATGTTTCGATTTAGTTAGAAATTAATTTGGAAAAAATTTTGAA
*
41906 AGACGATATTA
322 AAACGATATTA
* * *
41917 GAAGCGTGAAAACCCTTCAAT-TATTTTGGTATTGAATTATATAATTTTTTATGTGTATTGTGGC
1 GAAGCGTGAAAACCCTTCAATCT-TTTTGGCATTGAATTATAT-ATTTTTTGTGAGTATTGTGGC
* * * ** *
41981 AAAAAATTGAGTGAAAAACTTTT-GGGTCAG-TTTTTCAAAAATTTTGGTTGAAATCGTGTATTA
64 AAAAAATGGAG-GAAAAAATTTTCGGGTCAGTTTTTTCAAAAATTTTAGCCGAAATCGTGTACTA
* * *
42044 ACCATCATGATTTTTGGCTAAAAATGCGCTATGGGCCCCGGCTCAATTTTGCATAATTTTTAGTG
128 ACCATCATGATTTTTGGCTAAAAATGCGCTATGGGCCCCGGCTCAGTTTTGCATGATTTTTGGTG
* * *
42109 CGAAGACTCCTTGAAATATCTTTATTCATCTAACCAAATCTTAGCCGCAATGGGTTTTAAGGATT
193 CCAAGACTCCTTGAAATATCTTTATTCATCTAACCAAATCTCAGCCGCAAT-GGATTTAAGGATT
* *
42174 TGTTTTTTGCGAGCATCTGAATCATGTTTCGATTTACTTAGAAATTAATTTGGAAAAAATCTTGA
257 TG-TTTTTGCGAGCATCTGAATCATGTTTCGATTTAGTTAGAAATTAATTTGGAAAAAATTTTGA
42239 AAAACGATATTA
321 AAAACGATATTA
*
42251 GAAGCGTGAAATGCCCTTCAATCTTTTTGGCATTGAATTATATATTTTTTGTGAGTATTGTGGCA
1 GAAGCGTGAAA-ACCCTTCAATCTTTTTGGCATTGAATTATATATTTTTTGTGAGTATTGTGGCA
42316 AAAAATGGAGGAAAAAATTTTCGGGTCAGTTTTTTCAAAAATTTTAGCCGAAATCGTGTACTAAC
65 AAAAATGGAGGAAAAAATTTTCGGGTCAGTTTTTTCAAAAATTTTAGCCGAAATCGTGTACTAAC
* * *
42381 CATCATGATTTTTGGCTAAAAATGCACTATGGTGCCCCGACTAAGTTTTGCATGATTTTTGGTGC
130 CATCATGATTTTTGGCTAAAAATGCGCTATGG-GCCCCGGCTCAGTTTTGCATGATTTTTGGTGC
* *
42446 CGAA-ACTCCTTGAAATATCTTTATTCATCTAACCAAATCCCAGCCGCAATGGATTTAAGGAATT
194 C-AAGACTCCTTGAAATATCTTTATTCATCTAACCAAATCTCAGCCGCAATGGATTTAAGGATTT
*
42510 GTTTTTGCGAGTATCTGAATCATG-TTCGATTTAGTTAGAAATTAATTTGG-AAAAATTTTGAAA
258 GTTTTTGCGAGCATCTGAATCATGTTTCGATTTAGTTAGAAATTAATTTGGAAAAAATTTTGAAA
*
42573 GACGATATTA
323 AACGATATTA
*
42583 GAAGCGTGAAAACCCTTCAAT-TATTTTGGCATTGAATTATATAATTTTTTATGAGTATTGTGGC
1 GAAGCGTGAAAACCCTTCAATCT-TTTTGGCATTGAATTATAT-ATTTTTTGTGAGTATTGTGGC
* * * * *
42647 AAAAGATTGAGTAAAAAACTTTCGGGTCAGTTTTTTCAAAAATTTTCGCCGAAATCGTGTACT-A
64 AAAAAATGGAGGAAAAAATTTTCGGGTCAGTTTTTTCAAAAATTTTAGCCGAAATCGTGTACTAA
*
42711 -CATCATGATTTTTGGCTAAAAATGCGCTATGGGGCCCCGACTCAGTTTTGCATGATTTTTGGTG
129 CCATCATGATTTTTGGCTAAAAATGCGCTAT-GGGCCCCGGCTCAGTTTTGCATGATTTTTGGTG
* * * * *
42775 CTAAGACTCCTTGAAATATCTTTATTCATTTAATCAAATTTCAGCCGCAATGGGTTTAAGGATTT
193 CCAAGACTCCTTGAAATATCTTTATTCATCTAACCAAATCTCAGCCGCAATGGATTTAAGGATTT
* *
42840 GTTTTTGCGAACGTCTGAATCATGTTTCGATTTAGTTAGAAATTAATTTGGAAAAAATTTTGAAA
258 GTTTTTGCGAGCATCTGAATCATGTTTCGATTTAGTTAGAAATTAATTTGGAAAAAATTTTGAAA
42905 AACGATATTA
323 AACGATATTA
* * * * *
42915 AAAGCGCGAAAAAAAACCTTCAATCTTTCTT-GCGTTGAATCATATA--TTTTGTGAGTATTGTG
1 GAAGCGTG---AAAACCCTTCAATCTTT-TTGGCATTGAATTATATATTTTTTGTGAGTATTGTG
* * ** **
42977 GCAAAAAATGGAGGAAAAAATTTTTGGGTCCGTTTTTTTCAAAAATTTTAGCCGAAGCCCGAAAT
62 GCAAAAAATGGAGGAAAAAATTTTCGGGTCAG-TTTTTTCAAAAATTTTAGCCGAA-ATCG-TGT
* * ** * * ** * *
43042 CCTGTACGTTAATGGTTTTTGGCTAAAAATGCGTTCT-TGGATCCCGGCTTAGTTTTGCTTGATT
124 ACT-AACCATCATGATTTTTGGCTAAAAATGCG--CTATGGGCCCCGGCTCAGTTTTGCATGATT
*
43106 TTTGGTGTCAAGACTCCTTGAAATATCT
186 TTTGGTGCCAAGACTCCTTGAAATATCT
43134 CTAACGTTAC
Statistics
Matches: 1411, Mismatches: 103, Indels: 68
0.89 0.07 0.04
Matches are distributed among these distances:
329 2 0.00
330 136 0.10
331 61 0.04
332 397 0.28
333 233 0.17
334 279 0.20
335 145 0.10
336 83 0.06
337 3 0.00
338 69 0.05
339 1 0.00
340 2 0.00
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.37
Consensus pattern (332 bp):
GAAGCGTGAAAACCCTTCAATCTTTTTGGCATTGAATTATATATTTTTTGTGAGTATTGTGGCAA
AAAATGGAGGAAAAAATTTTCGGGTCAGTTTTTTCAAAAATTTTAGCCGAAATCGTGTACTAACC
ATCATGATTTTTGGCTAAAAATGCGCTATGGGCCCCGGCTCAGTTTTGCATGATTTTTGGTGCCA
AGACTCCTTGAAATATCTTTATTCATCTAACCAAATCTCAGCCGCAATGGATTTAAGGATTTGTT
TTTGCGAGCATCTGAATCATGTTTCGATTTAGTTAGAAATTAATTTGGAAAAAATTTTGAAAAAC
GATATTA
Found at i:44357 original size:14 final size:14
Alignment explanation
Indices: 44331--44368 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
44321 TAATTGATTA
44331 ATTTTTTTA-TAAT
1 ATTTTTTTATTAAT
44344 ATTTTTTTATTAAT
1 ATTTTTTTATTAAT
44358 -TTATTTTTATT
1 ATT-TTTTTATT
44369 TCAGCTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
ATTTTTTTATTAAT
Found at i:44580 original size:32 final size:32
Alignment explanation
Indices: 44544--44614 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 32
44534 AAATTGATAG
** * *
44544 ACAAAATAGTCCTCGAATTTTGACATAGAAGA
1 ACAAAATAACCCTCAAATTTTGACAAAGAAGA
* *
44576 ACAAAATAACCCTCAAATTTTGACAAAGTAGG
1 ACAAAATAACCCTCAAATTTTGACAAAGAAGA
44608 ACAAAAT
1 ACAAAAT
44615 GTTCTTTGAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.48, C:0.17, G:0.13, T:0.23
Consensus pattern (32 bp):
ACAAAATAACCCTCAAATTTTGACAAAGAAGA
Found at i:46115 original size:2 final size:2
Alignment explanation
Indices: 46108--46139 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
46098 GTTTAGTATC
46108 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
46140 TGCCTTGTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:59458 original size:13 final size:13
Alignment explanation
Indices: 59426--59459 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
59416 AGAAAAAATG
*
59426 CTATTTACCCCGC
1 CTATTTGCCCCGC
*
59439 CTATTTGCCCTGC
1 CTATTTGCCCCGC
59452 CTATTTGC
1 CTATTTGC
59460 ATCACTTGGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.12, C:0.38, G:0.12, T:0.38
Consensus pattern (13 bp):
CTATTTGCCCCGC
Found at i:74979 original size:45 final size:45
Alignment explanation
Indices: 74922--75072 Score: 284
Period size: 45 Copynumber: 3.4 Consensus size: 45
74912 GTCTTCTTTT
74922 CCTTGGCCTTGTCAGGGATAGGTTTTTCATCCTGGCTTTTCTTCA
1 CCTTGGCCTTGTCAGGGATAGGTTTTTCATCCTGGCTTTTCTTCA
74967 CCTTGGCCTTGTCAGGGATAGGTTTTTCATCCTGGCTTTTCTTCA
1 CCTTGGCCTTGTCAGGGATAGGTTTTTCATCCTGGCTTTTCTTCA
75012 CCTTGGCCTTGTCAGGGATAGGTTTTTCATCCTGGCTTTTCTTCA
1 CCTTGGCCTTGTCAGGGATAGGTTTTTCATCCTGGCTTTTCTTCA
* *
75057 CTTTGGCCTTCTCAGG
1 CCTTGGCCTTGTCAGG
75073 ACCAGGCGGC
Statistics
Matches: 104, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 104 1.00
ACGTcount: A:0.11, C:0.25, G:0.23, T:0.42
Consensus pattern (45 bp):
CCTTGGCCTTGTCAGGGATAGGTTTTTCATCCTGGCTTTTCTTCA
Done.