Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015791.1 Corchorus olitorius cultivar O-4 contig15824, 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: 68393
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:1009 original size:22 final size:22
Alignment explanation
Indices: 973--1177 Score: 147
Period size: 22 Copynumber: 9.2 Consensus size: 22
963 AAATCTATCA
*
973 GAAATTCTG-TAACC-TCGCTAT
1 GAAATTTTGATAACCTTC-CTAT
* *
994 GAAATTTTTATAACCTTCTTAT
1 GAAATTTTGATAACCTTCCTAT
**
1016 GAAATTTTGATAA-CTTTTTGAT
1 GAAATTTTGATAACCTTCCT-AT
*
1038 GAAATTTTAATAACCTGATCCTAT
1 GAAATTTTGATAACCT--TCCTAT
*
1062 GAAATTCTGATAA--TTACTCTAT
1 GAAATTTTGATAACCTT-C-CTAT
* *
1084 GAAATCTTGATAATCTTCCTAT
1 GAAATTTTGATAACCTTCCTAT
1106 GAAATTTTGATAACC-TCCATAT
1 GAAATTTTGATAACCTTCC-TAT
* *
1128 GAAAAATTCGATAA-CTTCCTTAT
1 G-AAATTTTGATAACCTTCC-TAT
* *
1151 GAAAATTTGGTAACC-TCCTTAT
1 GAAATTTTGATAACCTTCC-TAT
1173 GAAAT
1 GAAAT
1178 AATAATATCT
Statistics
Matches: 150, Mismatches: 20, Indels: 27
0.76 0.10 0.14
Matches are distributed among these distances:
20 1 0.01
21 16 0.11
22 93 0.62
23 23 0.15
24 15 0.10
25 2 0.01
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.40
Consensus pattern (22 bp):
GAAATTTTGATAACCTTCCTAT
Found at i:1129 original size:44 final size:43
Alignment explanation
Indices: 973--1208 Score: 156
Period size: 44 Copynumber: 5.3 Consensus size: 43
963 AAATCTATCA
* * * *
973 GAAATTCTG-TAACCTCGCTATGAAATTTTTATAACCTTCTTAT
1 GAAATTTTGATAACCTC-CTATGAAATATTAATAACCTTCCTAT
* ** *
1016 GAAATTTTGATAACTTTTTGATGAAATTTTAATAACCTGATCCTAT
1 GAAATTTTGATAACCTCCT-ATGAAATATTAATAACCT--TCCTAT
* * * * *
1062 GAAATTCTGATAA-TTACTCTATGAAATCTTGATAATCTTCCTAT
1 GAAATTTTGATAACCT-C-CTATGAAATATTAATAACCTTCCTAT
* *
1106 GAAATTTTGATAACCTCCATATGAAAAATTCGATAA-CTTCCTTAT
1 GAAATTTTGATAACCTCC-TATGAAATATT-AATAACCTTCC-TAT
* * * * *
1151 GAAAATTTGGTAACCTCCTTATGAAATAATAAT-ATCTTCTTAT
1 GAAATTTTGATAACCTCC-TATGAAATATTAATAACCTTCCTAT
* *
1194 TATATTTTGATAACC
1 GAAATTTTGATAACC
1209 ACACAGAGAC
Statistics
Matches: 155, Mismatches: 27, Indels: 22
0.76 0.13 0.11
Matches are distributed among these distances:
43 25 0.16
44 61 0.39
45 36 0.23
46 32 0.21
47 1 0.01
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (43 bp):
GAAATTTTGATAACCTCCTATGAAATATTAATAACCTTCCTAT
Found at i:1135 original size:68 final size:65
Alignment explanation
Indices: 1003--1177 Score: 153
Period size: 68 Copynumber: 2.6 Consensus size: 65
993 TGAAATTTTT
* **
1003 ATAACCTT-CTTATGAAATTTTGATAACTTTTTGATGAAATTTTAATAACCTGATCCTATGAAAT
1 ATAA-CTTACTTATGAAATCTTGATAACTTCCTGATGAAATTTTAATAACC--ATCCTATGAAAT
1067 TCTG
63 TC-G
*
1071 ATAA-TTACTCTATGAAATCTTGATAATCTTCCT-ATGAAATTTTGATAACC-TCCATATGAAAA
1 ATAACTTACT-TATGAAATCTTGATAA-CTTCCTGATGAAATTTTAATAACCATCC-TATG--AA
1133 ATTCG
61 ATTCG
* * * *
1138 ATAACTTCCTTATGAAAAT-TTGGTAACCTCCTTATGAAAT
1 ATAACTTACTTATG-AAATCTTGATAACTTCCTGATGAAAT
1178 AATAATATCT
Statistics
Matches: 91, Mismatches: 7, Indels: 19
0.78 0.06 0.16
Matches are distributed among these distances:
65 3 0.03
66 11 0.12
67 24 0.26
68 49 0.54
69 4 0.04
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.39
Consensus pattern (65 bp):
ATAACTTACTTATGAAATCTTGATAACTTCCTGATGAAATTTTAATAACCATCCTATGAAATTCG
Found at i:1726 original size:6 final size:6
Alignment explanation
Indices: 1715--1749 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
1705 GTACTTTTAT
* *
1715 ATATAG ATATAG ATATAG ATATGG ATATAC ATATA
1 ATATAG ATATAG ATATAG ATATAG ATATAG ATATA
1750 AATAATAAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.49, C:0.03, G:0.14, T:0.34
Consensus pattern (6 bp):
ATATAG
Found at i:10161 original size:18 final size:17
Alignment explanation
Indices: 10137--10176 Score: 71
Period size: 18 Copynumber: 2.3 Consensus size: 17
10127 TTTTGTGGAT
10137 GTCTTAACTATATTTAG
1 GTCTTAACTATATTTAG
10154 GCTCTTAACTATATTTAG
1 G-TCTTAACTATATTTAG
10172 GTCTT
1 GTCTT
10177 TCTCGATTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.25, C:0.15, G:0.12, T:0.47
Consensus pattern (17 bp):
GTCTTAACTATATTTAG
Found at i:13131 original size:15 final size:15
Alignment explanation
Indices: 13111--13139 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
13101 AAAGTACCCT
13111 TATAATTAATTAAAG
1 TATAATTAATTAAAG
13126 TATAATTAATTAAA
1 TATAATTAATTAAA
13140 TACATGAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.41
Consensus pattern (15 bp):
TATAATTAATTAAAG
Found at i:13672 original size:13 final size:12
Alignment explanation
Indices: 13652--13684 Score: 57
Period size: 13 Copynumber: 2.7 Consensus size: 12
13642 ATAATAATGT
13652 TATATTATATTA
1 TATATTATATTA
13664 TATTATTATATTA
1 TA-TATTATATTA
13677 TATATTAT
1 TATATTAT
13685 TAATAAACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 8 0.40
13 12 0.60
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
TATATTATATTA
Found at i:13840 original size:17 final size:17
Alignment explanation
Indices: 13818--13851 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
13808 AAATCCGAGC
13818 CCGAGCCCGAACACGAT
1 CCGAGCCCGAACACGAT
*
13835 CCGAGCCCGAACCCGAT
1 CCGAGCCCGAACACGAT
13852 TTAACCCGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.44, G:0.24, T:0.06
Consensus pattern (17 bp):
CCGAGCCCGAACACGAT
Found at i:22632 original size:22 final size:22
Alignment explanation
Indices: 22607--22675 Score: 72
Period size: 21 Copynumber: 3.2 Consensus size: 22
22597 CTGTAAATTA
22607 AGAAATACTCAACTCAAATCAT
1 AGAAATACTCAACTCAAATCAT
* * * *
22629 AGAAA-ATTC-TCTGTAAATTA-
1 AGAAATACTCAACT-CAAATCAT
22649 AGAAATACTCAACTCAAATCAT
1 AGAAATACTCAACTCAAATCAT
22671 AGAAA
1 AGAAA
22676 ATTCTTTGTA
Statistics
Matches: 35, Mismatches: 8, Indels: 8
0.69 0.16 0.16
Matches are distributed among these distances:
20 7 0.20
21 16 0.46
22 12 0.34
ACGTcount: A:0.51, C:0.17, G:0.07, T:0.25
Consensus pattern (22 bp):
AGAAATACTCAACTCAAATCAT
Found at i:22649 original size:42 final size:42
Alignment explanation
Indices: 22590--22710 Score: 224
Period size: 42 Copynumber: 2.9 Consensus size: 42
22580 TAAGTCTTGT
22590 AAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATAGA
1 AAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATAGA
22632 AAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATAGA
1 AAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATAGA
* *
22674 AAATTCTTTGTAAATTAAGAAATACTCAACTGAAATC
1 AAATTCTCTGTAAATTAAGAAATACTCAACTCAAATC
22711 CTGATCCTTA
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 77 1.00
ACGTcount: A:0.47, C:0.16, G:0.07, T:0.30
Consensus pattern (42 bp):
AAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATAGA
Found at i:22848 original size:56 final size:57
Alignment explanation
Indices: 22776--22892 Score: 227
Period size: 57 Copynumber: 2.1 Consensus size: 57
22766 TTTATTTTGT
22776 AGAATAATTAAGTAGAGATA-GGGGGATAGGATTTATTATAACATTTATTGTGTGAA
1 AGAATAATTAAGTAGAGATAGGGGGGATAGGATTTATTATAACATTTATTGTGTGAA
22832 AGAATAATTAAGTAGAGATAGGGGGGATAGGATTTATTATAACATTTATTGTGTGAA
1 AGAATAATTAAGTAGAGATAGGGGGGATAGGATTTATTATAACATTTATTGTGTGAA
22889 AGAA
1 AGAA
22893 AACAGATAAT
Statistics
Matches: 60, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
56 20 0.33
57 40 0.67
ACGTcount: A:0.40, C:0.02, G:0.26, T:0.32
Consensus pattern (57 bp):
AGAATAATTAAGTAGAGATAGGGGGGATAGGATTTATTATAACATTTATTGTGTGAA
Found at i:25070 original size:76 final size:76
Alignment explanation
Indices: 24920--25071 Score: 175
Period size: 76 Copynumber: 2.0 Consensus size: 76
24910 ACAAGGGCCC
** * *
24920 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCTTGAGTACCCAGGT
1 CGACTCCACCTGGGCGCCCACATGGTTGCCTAAAGCACCCATGTGGTTTGCCTGAGTACCCAGAT
*
24985 GGGCAGTGTCA
66 GAGCAGTGTCA
* * *
24996 CGACTCCAGCTGGGTGCCCACATGGTTTGTCTAAAG-ACCCATGT-GTTTCGCCTGA-TCACCCA
1 CGACTCCACCTGGGCGCCCACATGG-TTGCCTAAAGCACCCATGTGGTTT-GCCTGAGT-ACCCA
*
25058 GATGAGCTGTGTCA
63 GATGAGCAGTGTCA
25072 TAGCTCGGTA
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
75 5 0.08
76 52 0.81
77 7 0.11
ACGTcount: A:0.18, C:0.30, G:0.28, T:0.25
Consensus pattern (76 bp):
CGACTCCACCTGGGCGCCCACATGGTTGCCTAAAGCACCCATGTGGTTTGCCTGAGTACCCAGAT
GAGCAGTGTCA
Found at i:32727 original size:20 final size:20
Alignment explanation
Indices: 32674--32727 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 20
32664 TATTAACTTT
*
32674 TAAATATAGTAAAAAAAATC
1 TAAATATAGTAAAAAAAATA
*
32694 TGAATATA-TAAAAAAATAATA
1 TAAATATAGT-AAAAAA-AATA
32715 TAAATA-AGTAAAA
1 TAAATATAGTAAAA
32728 GCTTTAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
19 1 0.04
20 18 0.64
21 9 0.32
ACGTcount: A:0.67, C:0.02, G:0.06, T:0.26
Consensus pattern (20 bp):
TAAATATAGTAAAAAAAATA
Found at i:37622 original size:30 final size:30
Alignment explanation
Indices: 37587--37645 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
37577 GATATTTTGA
*
37587 TATGTCATTCTTTAATAACTTTAGAAATAC
1 TATGTCATTCTTAAATAACTTTAGAAATAC
37617 TATGTCATTCTTAAATAACTTTAGAAATA
1 TATGTCATTCTTAAATAACTTTAGAAATA
37646 GTTGCAAAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.42
Consensus pattern (30 bp):
TATGTCATTCTTAAATAACTTTAGAAATAC
Found at i:38719 original size:2 final size:2
Alignment explanation
Indices: 38712--38745 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
38702 TAATATGCAG
38712 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
38746 CTACTTTGTT
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:41989 original size:21 final size:19
Alignment explanation
Indices: 41963--42017 Score: 74
Period size: 21 Copynumber: 2.8 Consensus size: 19
41953 CGCTGTTCTA
41963 ATAATCTCATCTGTACAGT
1 ATAATCTCATCTGTACAGT
*
41982 ATCCAATCTAATCTGTACAGT
1 AT--AATCTCATCTGTACAGT
*
42003 GTAATCTCATCTGTA
1 ATAATCTCATCTGTA
42018 GAGTTGCTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
19 14 0.45
21 17 0.55
ACGTcount: A:0.31, C:0.22, G:0.11, T:0.36
Consensus pattern (19 bp):
ATAATCTCATCTGTACAGT
Found at i:44207 original size:437 final size:433
Alignment explanation
Indices: 43325--44164 Score: 1067
Period size: 440 Copynumber: 1.9 Consensus size: 433
43315 TAGAATTTGG
* * *
43325 AAAGGACTAAGTAGCATGAAATAGAAAAGTATGAGGGTGATTTGATAACTAATTCAAATAAGAAA
1 AAAGGACTAAGTAACATGAAATAGAAAAGTATGAGGGTCATTTGATAAATAATTCAAATAAGAAA
*
43390 ATATTTGTTAATGGGATCTTGAAACATAAAAATTCCCTTTTGAACCCTTCATGAAACTCGTAGAT
66 ATATTTGTTAATGGGATCTTGAAACATAAAAATTCCCTTTTGAACCCTTCACGAAACTCGTAGAT
* * * *
43455 CAAATTAACTTTCGGGTTCTTCATGAAATTCGTAGATTATACAGTAACCTTTTAACCGACACTTA
131 CAAATTAACTTTCGGGTTCTTCATGAAAGTCGTAAATCATACAATAACCTTTTAACCGACACTTA
* * * * * * *
43520 AATAACTTTAATTGGACATATGGATCGAAAACTATATGTTATTAAATAAACCAACAATCGAAACG
196 AATAACTTCAATCGGACATATGGATCAAAAACTATACGATATTAAATAAACCAACAATCAAAACC
* * *** *
43585 AACAAATTTAGGAAGCATTTTTTTGAATTGAAACATAAAAATTTGCTTTTGAGTCCTTCATGAAA
261 AACAAATTTAGGAAGCACTTTTTAGAACCAAAACATAAAAATTTGCTTCTGAG--CTTCATGAAA
* *
43650 GTTGTAGATCATGAAATTACCTTTTAATAGACACATGAATCAACTTAATCGGACAAATAGAACAA
324 G-TGTAGATCATGAAATTACCTTTTAATAGACACACGAATCAACTTAATCGGACAAATAGAAAAA
* * * *
43715 AAAATAAGAAAAATAAAGCTTAAAGGTTAGATTAAGATAGAATTTAT
388 AAAATAACAAAAATAAAGC-TAAAGGTTAAATTAACATAGAATTGAT
*
43762 AAAGGACTAAGTAATAT-AAAGTAGAAAAGTATGAGGGTCATTTGATAAATAA-TCAAAATAAGA
1 AAAGGACTAAGTAACATGAAA-TAGAAAAGTATGAGGGTCATTTGATAAATAATTC-AAATAAGA
* *
43825 AAATGTTTGTTAATGGAGATCTTGAAACATAAAAATTCCCTTTTTGAACCTTTCACGAAACTCGT
64 AAATATTTGTTAATGG-GATCTTGAAACATAAAAATTCCC-TTTTGAACCCTTCACGAAACTCGT
* *
43890 AGATCAAATTTAGCTTTCGGG-TCATTCATGAAAGTCGTAAATCATGCAATAACCTTTTAACCGA
127 AGATCAAA-TTAACTTTCGGGTTC-TTCATGAAAGTCGTAAATCATACAATAACCTTTTAACCGA
* * * * **
43954 CACTTCAATAACTTCAATCGGACATGTGGA-CAAAAAATTATACGATATTAAATTAACCGGCAAT
190 CACTTAAATAACTTCAATCGGACATATGGATC-AAAAACTATACGATATTAAATAAACCAACAAT
* *
44018 CAAAACCATA-AAATTTTGGAAGCACTTTTTAGAACCAAAACATGTTAAAA-TTGACTTCTGAG-
254 CAAAACCA-ACAAATTTAGGAAGCACTTTTTAGAACCAAAACA--TAAAAATTTG-CTTCTGAGC
* *
44080 TTC-T-TAA-TG-AGATCATGAAATTACCTTTTAATAGACACCCGAATC-ACTTTAATCGGACAA
315 TTCATGAAAGTGTAGATCATGAAATTACCTTTTAATAGACACACGAATCAAC-TTAATCGGACAA
44140 ATAGAAAAAAAAAT-ACAAAAATAAA
379 ATAGAAAAAAAAATAACAAAAATAAA
44165 AGGCAACGCG
Statistics
Matches: 352, Mismatches: 39, Indels: 28
0.84 0.09 0.07
Matches are distributed among these distances:
433 12 0.03
434 59 0.17
435 2 0.01
436 5 0.01
437 69 0.20
438 24 0.07
439 36 0.10
440 129 0.37
441 4 0.01
442 12 0.03
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (433 bp):
AAAGGACTAAGTAACATGAAATAGAAAAGTATGAGGGTCATTTGATAAATAATTCAAATAAGAAA
ATATTTGTTAATGGGATCTTGAAACATAAAAATTCCCTTTTGAACCCTTCACGAAACTCGTAGAT
CAAATTAACTTTCGGGTTCTTCATGAAAGTCGTAAATCATACAATAACCTTTTAACCGACACTTA
AATAACTTCAATCGGACATATGGATCAAAAACTATACGATATTAAATAAACCAACAATCAAAACC
AACAAATTTAGGAAGCACTTTTTAGAACCAAAACATAAAAATTTGCTTCTGAGCTTCATGAAAGT
GTAGATCATGAAATTACCTTTTAATAGACACACGAATCAACTTAATCGGACAAATAGAAAAAAAA
ATAACAAAAATAAAGCTAAAGGTTAAATTAACATAGAATTGAT
Found at i:45563 original size:2 final size:2
Alignment explanation
Indices: 45556--45605 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
45546 ATATTTAGCC
*
45556 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
45598 AT AT AT AT
1 AT AT AT AT
45606 GTTTATACCT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:47269 original size:51 final size:51
Alignment explanation
Indices: 47172--47269 Score: 119
Period size: 51 Copynumber: 1.9 Consensus size: 51
47162 CTTCATATTT
* **
47172 TCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCTTTTAGTGTTTTTC
1 TCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCGTACAGTGTTTTTC
* *
47223 TCTTGTTTCA-ATCTTGTCTCCGGACATACAAACACT-GTACACGTGTT
1 TCTTGTTT-AGATCTTGTCTCAGGACAAACAAACACTCGTACA-GTGTT
47270 CTTCATTCAG
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
50 2 0.05
51 37 0.93
52 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.14, T:0.40
Consensus pattern (51 bp):
TCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCGTACAGTGTTTTTC
Found at i:49481 original size:22 final size:22
Alignment explanation
Indices: 49456--49595 Score: 102
Period size: 22 Copynumber: 6.3 Consensus size: 22
49446 ATGATCACCG
* *
49456 AAATTTCGTAGAGTGGTTATCA
1 AAATTTCATAGAGAGGTTATCA
* *
49478 AAATTTCAAAGAAAGGTTATCA
1 AAATTTCATAGAGAGGTTATCA
* * **
49500 AATTTTTCATAGTGTTGTTATCAA
1 AA-ATTTCATAGAGAGGTTATC-A
*
49524 AAAATTCATAG-GAAGGTTATCA
1 AAATTTCATAGAG-AGGTTATCA
* * *
49546 GAATTTTATAGCGAGGTTATCA
1 AAATTTCATAGAGAGGTTATCA
* * * *
49568 GAATTTCGTAGTGTGGTTATCA
1 AAATTTCATAGAGAGGTTATCA
49590 AAATTT
1 AAATTT
49596 TCTAAAGAAG
Statistics
Matches: 92, Mismatches: 22, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
22 62 0.67
23 27 0.29
24 3 0.03
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.37
Consensus pattern (22 bp):
AAATTTCATAGAGAGGTTATCA
Found at i:50202 original size:23 final size:23
Alignment explanation
Indices: 50176--50226 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 23
50166 GCATTCAGCC
** *
50176 AAATTTTTTTAGTGTGGTGATCA
1 AAATTTTCATAGTGAGGTGATCA
*
50199 AAA-TTTCATAGTGAGGTTATCA
1 AAATTTTCATAGTGAGGTGATCA
50221 AAATTT
1 AAATTT
50227 AATGTGGAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.33, C:0.06, G:0.18, T:0.43
Consensus pattern (23 bp):
AAATTTTCATAGTGAGGTGATCA
Found at i:50210 original size:22 final size:22
Alignment explanation
Indices: 50185--50226 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
50175 CAAATTTTTT
*
50185 TAGTGTGGTGATCAAAATTTCA
1 TAGTGAGGTGATCAAAATTTCA
*
50207 TAGTGAGGTTATCAAAATTT
1 TAGTGAGGTGATCAAAATTT
50227 AATGTGGAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.07, G:0.21, T:0.38
Consensus pattern (22 bp):
TAGTGAGGTGATCAAAATTTCA
Found at i:50562 original size:20 final size:20
Alignment explanation
Indices: 50494--50591 Score: 81
Period size: 22 Copynumber: 4.7 Consensus size: 20
50484 TTTCGCCATC
* *
50494 TCAAAATTTCATAGTTTAGTTT
1 TCAAAATTTCATAGTGT-G-GT
* *
50516 TCAAAATTTTATAG-GGGGTT
1 TCAAAATTTCATAGTGTGG-T
50536 ATCAAAATTTCATAGTGTGGT
1 -TCAAAATTTCATAGTGTGGT
* *
50557 TCAAAATTTCATAGGGTGAT
1 TCAAAATTTCATAGTGTGGT
50577 TAACAAAATTTCATA
1 T--CAAAATTTCATA
50592 ATGAGATTAT
Statistics
Matches: 63, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
20 21 0.33
21 14 0.22
22 28 0.44
ACGTcount: A:0.36, C:0.09, G:0.15, T:0.40
Consensus pattern (20 bp):
TCAAAATTTCATAGTGTGGT
Found at i:50586 original size:22 final size:21
Alignment explanation
Indices: 50517--50591 Score: 91
Period size: 20 Copynumber: 3.6 Consensus size: 21
50507 GTTTAGTTTT
*
50517 CAAAATTTTATAGGG-GGTTA
1 CAAAATTTCATAGGGTGGTTA
*
50537 TCAAAATTTCATAGTGTGGTT-
1 -CAAAATTTCATAGGGTGGTTA
*
50558 CAAAATTTCATAGGGTGATTAA
1 CAAAATTTCATAGGGTGGTT-A
50580 CAAAATTTCATA
1 CAAAATTTCATA
50592 ATGAGATTAT
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
20 18 0.38
21 13 0.28
22 16 0.34
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.36
Consensus pattern (21 bp):
CAAAATTTCATAGGGTGGTTA
Found at i:50606 original size:22 final size:22
Alignment explanation
Indices: 50558--50600 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
50548 TAGTGTGGTT
* *
50558 CAAAATTTCATAGGGTGATTAA
1 CAAAATTTCATAAGGAGATTAA
*
50580 CAAAATTTCATAATGAGATTA
1 CAAAATTTCATAAGGAGATTA
50601 TAAAAAAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.44, C:0.09, G:0.14, T:0.33
Consensus pattern (22 bp):
CAAAATTTCATAAGGAGATTAA
Found at i:51138 original size:22 final size:22
Alignment explanation
Indices: 51108--51164 Score: 55
Period size: 22 Copynumber: 2.6 Consensus size: 22
51098 TAATTACCAT
*
51108 AATTCCATATGAAGAT-TATCAA
1 AATTTCATATGAAG-TGTATCAA
* *
51130 ATTTTCATAGTG-TGTGTATCAA
1 AATTTCATA-TGAAGTGTATCAA
51152 AATTTCATATGAA
1 AATTTCATATGAA
51165 TATTTAATTT
Statistics
Matches: 27, Mismatches: 5, Indels: 6
0.71 0.13 0.16
Matches are distributed among these distances:
21 3 0.11
22 22 0.81
23 2 0.07
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.39
Consensus pattern (22 bp):
AATTTCATATGAAGTGTATCAA
Found at i:51480 original size:23 final size:23
Alignment explanation
Indices: 51454--51504 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 23
51444 GCATTCAGCC
** *
51454 AAATTTTTTTAGTGTGGTGATCA
1 AAATTTTCATAGTGAGGTGATCA
*
51477 AAA-TTTCATAGTGAGGTTATCA
1 AAATTTTCATAGTGAGGTGATCA
51499 AAATTT
1 AAATTT
51505 AATGTGGAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.33, C:0.06, G:0.18, T:0.43
Consensus pattern (23 bp):
AAATTTTCATAGTGAGGTGATCA
Found at i:51488 original size:22 final size:22
Alignment explanation
Indices: 51463--51504 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
51453 CAAATTTTTT
*
51463 TAGTGTGGTGATCAAAATTTCA
1 TAGTGAGGTGATCAAAATTTCA
*
51485 TAGTGAGGTTATCAAAATTT
1 TAGTGAGGTGATCAAAATTT
51505 AATGTGGAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.07, G:0.21, T:0.38
Consensus pattern (22 bp):
TAGTGAGGTGATCAAAATTTCA
Found at i:51837 original size:20 final size:20
Alignment explanation
Indices: 51769--51866 Score: 81
Period size: 22 Copynumber: 4.7 Consensus size: 20
51759 TTTCGCCATC
* *
51769 TCAAAATTTCATAGTTTAGTTT
1 TCAAAATTTCATAGTGT-G-GT
* *
51791 TCAAAATTTTATAG-GGGGTT
1 TCAAAATTTCATAGTGTGG-T
51811 ATCAAAATTTCATAGTGTGGT
1 -TCAAAATTTCATAGTGTGGT
* *
51832 TCAAAATTTCATAGGGTGAT
1 TCAAAATTTCATAGTGTGGT
51852 TAACAAAATTTCATA
1 T--CAAAATTTCATA
51867 ATGAGATTAT
Statistics
Matches: 63, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
20 21 0.33
21 14 0.22
22 28 0.44
ACGTcount: A:0.36, C:0.09, G:0.15, T:0.40
Consensus pattern (20 bp):
TCAAAATTTCATAGTGTGGT
Found at i:51861 original size:22 final size:21
Alignment explanation
Indices: 51792--51866 Score: 91
Period size: 20 Copynumber: 3.6 Consensus size: 21
51782 GTTTAGTTTT
*
51792 CAAAATTTTATAGGG-GGTTA
1 CAAAATTTCATAGGGTGGTTA
*
51812 TCAAAATTTCATAGTGTGGTT-
1 -CAAAATTTCATAGGGTGGTTA
*
51833 CAAAATTTCATAGGGTGATTAA
1 CAAAATTTCATAGGGTGGTT-A
51855 CAAAATTTCATA
1 CAAAATTTCATA
51867 ATGAGATTAT
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
20 18 0.38
21 13 0.28
22 16 0.34
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.36
Consensus pattern (21 bp):
CAAAATTTCATAGGGTGGTTA
Found at i:51881 original size:22 final size:22
Alignment explanation
Indices: 51833--51875 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
51823 TAGTGTGGTT
* *
51833 CAAAATTTCATAGGGTGATTAA
1 CAAAATTTCATAAGGAGATTAA
*
51855 CAAAATTTCATAATGAGATTA
1 CAAAATTTCATAAGGAGATTA
51876 TAAAAAAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.44, C:0.09, G:0.14, T:0.33
Consensus pattern (22 bp):
CAAAATTTCATAAGGAGATTAA
Found at i:55104 original size:16 final size:17
Alignment explanation
Indices: 55076--55125 Score: 54
Period size: 16 Copynumber: 3.1 Consensus size: 17
55066 TGGTTTGTTC
*
55076 GGGTTCAGATTTTCTTA
1 GGGTTCAGGTTTTCTTA
55093 GGG-TCAGGTTTT-TT-
1 GGGTTCAGGTTTTCTTA
55107 GGGTTC-GGATTTTCTTA
1 GGGTTCAGG-TTTTCTTA
55124 GG
1 GG
55126 TTTGGGTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
14 5 0.18
15 8 0.29
16 10 0.36
17 5 0.18
ACGTcount: A:0.12, C:0.10, G:0.32, T:0.46
Consensus pattern (17 bp):
GGGTTCAGGTTTTCTTA
Found at i:55111 original size:31 final size:31
Alignment explanation
Indices: 55067--55143 Score: 91
Period size: 31 Copynumber: 2.4 Consensus size: 31
55057 TGAATTCGCT
*
55067 GGTTTGTTCGGGTTCAGATTTTCTTAGGGTCA
1 GGTTT-TTTGGGTTCAGATTTTCTTAGGGTCA
* * **
55099 GGTTTTTTGGGTTCGGATTTTCTTAGGTTTG
1 GGTTTTTTGGGTTCAGATTTTCTTAGGGTCA
55130 GGTTTTTCTGGGTT
1 GGTTTTT-TGGGTT
55144 TGGTTTTTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
31 28 0.72
32 11 0.28
ACGTcount: A:0.08, C:0.09, G:0.32, T:0.51
Consensus pattern (31 bp):
GGTTTTTTGGGTTCAGATTTTCTTAGGGTCA
Found at i:55135 original size:16 final size:15
Alignment explanation
Indices: 55099--55161 Score: 54
Period size: 16 Copynumber: 4.1 Consensus size: 15
55089 CTTAGGGTCA
* *
55099 GGTTTTTTGGGTTCG
1 GGTTTTTTAGGTTTG
*
55114 GATTTTCTTAGGTTTG
1 GGTTTT-TTAGGTTTG
*
55130 GGTTTTTCTGGGTTTG
1 GGTTTTT-TAGGTTTG
* *
55146 GTTTTTTTAGATTTG
1 GGTTTTTTAGGTTTG
55161 G
1 G
55162 ATTCGGACGG
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
15 13 0.34
16 25 0.66
ACGTcount: A:0.06, C:0.05, G:0.32, T:0.57
Consensus pattern (15 bp):
GGTTTTTTAGGTTTG
Found at i:55161 original size:31 final size:31
Alignment explanation
Indices: 55067--55161 Score: 84
Period size: 31 Copynumber: 3.0 Consensus size: 31
55057 TGAATTCGCT
* * ** **
55067 GGTTTGTTCGGGTTCAGATTTTCTTAGGGTCA
1 GGTTT-TTTGGGTTCGGATTTTCTTAGATTTG
*
55099 GGTTTTTTGGGTTCGGATTTTCTTAGGTTTG
1 GGTTTTTTGGGTTCGGATTTTCTTAGATTTG
* *
55130 GGTTTTTCTGGGTTTGG-TTTTTTTAGATTTG
1 GGTTTTT-TGGGTTCGGATTTTCTTAGATTTG
55161 G
1 G
55162 ATTCGGACGG
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
31 41 0.76
32 13 0.24
ACGTcount: A:0.08, C:0.07, G:0.32, T:0.53
Consensus pattern (31 bp):
GGTTTTTTGGGTTCGGATTTTCTTAGATTTG
Found at i:57910 original size:204 final size:203
Alignment explanation
Indices: 57505--57894 Score: 575
Period size: 206 Copynumber: 1.9 Consensus size: 203
57495 TTTTATAAGA
*
57505 GTAATTATTTGATATACCGGCGGTGTAAATTTTGGACTCCAAAAGCGGGTTGTGGAGTTGACACA
1 GTAATTATTTGATACACCGGCGGTGTAAATTTTGGACTCCAAAAGCGGGTTGTGGAGTTGACACA
* * * * *
57570 TGTCTATTTTCTGAATTAATTAAATTTTAAATATTTCAATTTAATCTCTAGGGGACACATGTCAC
66 TGTCCATTTTCTGAATTAAATAAATTTTAAATATTTCAATCTAATCCCTAGAGGACACATGTCAC
* * * *
57635 CCTTTAAGACCCGCTTGTGCAGTCTGCTAAACTTCACTGACGACGTATTTTATATAAACCCATTT
131 CCTTCAAGACCCACTTGTGCAGTCTGCTAAACTCCACTGACGACGTATTGTATATAAACCCA-TT
57700 TATAATTGG
195 TATAATTGG
* *
57709 GTAATTATTTGATACACCGGCGGTGTAAATTTTGGACTTCACAAGCGGGTTGTGGAGTTGACACA
1 GTAATTATTTGATACACCGGCGGTGTAAATTTTGGACTCCAAAAGCGGGTTGTGGAGTTGACAC-
* * *
57774 TATGTCCATTTTTTGAATTAAATAAGTTTTAAATATTTCAATCTAGTCCCTAGAGGACACATGTC
65 -ATGTCCATTTTCTGAATTAAATAAATTTTAAATATTTCAATCTAATCCCTAGAGGACACATGTC
* * *
57839 ACCCTTC-AGAACCCACTTGTGTAGTCTGTTAAACTCCACTGACGATGTATTGTATA
129 ACCCTTCAAG-ACCCACTTGTGCAGTCTGCTAAACTCCACTGACGACGTATTGTATA
57895 ATTTACCTTT
Statistics
Matches: 165, Mismatches: 18, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
204 61 0.37
205 2 0.01
206 102 0.62
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (203 bp):
GTAATTATTTGATACACCGGCGGTGTAAATTTTGGACTCCAAAAGCGGGTTGTGGAGTTGACACA
TGTCCATTTTCTGAATTAAATAAATTTTAAATATTTCAATCTAATCCCTAGAGGACACATGTCAC
CCTTCAAGACCCACTTGTGCAGTCTGCTAAACTCCACTGACGACGTATTGTATATAAACCCATTT
ATAATTGG
Found at i:59467 original size:26 final size:25
Alignment explanation
Indices: 59435--59487 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
59425 TGACAGACTA
*
59435 TATATATAATATAATTTTAAAAATAT
1 TATATATAATA-AAATTTAAAAATAT
* *
59461 TATATATATTAAAATTTATAAATAT
1 TATATATAATAAAATTTAAAAATAT
59486 TA
1 TA
59488 ATTTTATATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
25 14 0.58
26 10 0.42
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (25 bp):
TATATATAATAAAATTTAAAAATAT
Found at i:59485 original size:16 final size:17
Alignment explanation
Indices: 59454--59488 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
59444 TATAATTTTA
*
59454 AAAATATTATATATATT
1 AAAATATTATAAATATT
59471 AAAAT-TTATAAATATT
1 AAAATATTATAAATATT
59487 AA
1 AA
59489 TTTTATATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AAAATATTATAAATATT
Found at i:60214 original size:11 final size:11
Alignment explanation
Indices: 60198--60222 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
60188 AAGTATTCAG
60198 AATTCTATATA
1 AATTCTATATA
60209 AATTCTATATA
1 AATTCTATATA
60220 AAT
1 AAT
60223 ATATTCTTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (11 bp):
AATTCTATATA
Found at i:60293 original size:24 final size:24
Alignment explanation
Indices: 60266--60314 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
60256 GTTCCATTTA
60266 ATTTCATATACATAACTTGATACT
1 ATTTCATATACATAACTTGATACT
60290 ATTTCATATACATAACTTGATACT
1 ATTTCATATACATAACTTGATACT
60314 A
1 A
60315 GTTTATGGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.39, C:0.16, G:0.04, T:0.41
Consensus pattern (24 bp):
ATTTCATATACATAACTTGATACT
Found at i:64992 original size:2 final size:2
Alignment explanation
Indices: 64987--65017 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
64977 TAATGCGTAC
64987 TA TA 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 TA TA T
65018 TAGATAATGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:66361 original size:44 final size:44
Alignment explanation
Indices: 66311--66435 Score: 169
Period size: 44 Copynumber: 2.8 Consensus size: 44
66301 TGACAATCAA
* * * * *
66311 ACCAAAATTACATAGAAAGATTATCAAAATTTCGTAGTGTGGTT
1 ACCAAAATTTCATATAGAGATTATCAAAATTTCATAGTGTAGTT
*
66355 ACCAAAATTTCATATAGAGATTATCAAAACTTCATAGTGTAGTT
1 ACCAAAATTTCATATAGAGATTATCAAAATTTCATAGTGTAGTT
* * *
66399 ATCAAAATTTCATATAGAGGTTACCAAAATTTCATAG
1 ACCAAAATTTCATATAGAGATTATCAAAATTTCATAG
66436 GGAGGGAGGT
Statistics
Matches: 71, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 71 1.00
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.33
Consensus pattern (44 bp):
ACCAAAATTTCATATAGAGATTATCAAAATTTCATAGTGTAGTT
Found at i:66440 original size:22 final size:22
Alignment explanation
Indices: 66311--66547 Score: 116
Period size: 22 Copynumber: 10.9 Consensus size: 22
66301 TGACAATCAA
* * *
66311 ACCAAAATTACATAGAAAGATT
1 ACCAAAATTTCATAGAGAGGTT
* * * *
66333 ATCAAAATTTCGTAGTGTGGTT
1 ACCAAAATTTCATAGAGAGGTT
* *
66355 ACCAAAATTTCATATAGAGATT
1 ACCAAAATTTCATAGAGAGGTT
* * *
66377 ATCAAAACTTCATAGTGTA-GTT
1 ACCAAAATTTCATAGAG-AGGTT
* *
66399 ATCAAAATTTCATATAGAGGTT
1 ACCAAAATTTCATAGAGAGGTT
66421 ACCAAAATTTCATAGGGAGGGAGGTT
1 ACCAAAATTTCATA--GA--GAGGTT
* *
66447 ACCAAAA-TT--T---GTGCTT
1 ACCAAAATTTCATAGAGAGGTT
* *
66463 ATCAAAATTTCCTAGAGAGGTT
1 ACCAAAATTTCATAGAGAGGTT
* *
66485 A-CAAAATTTTATAGGGAGGTT
1 ACCAAAATTTCATAGAGAGGTT
** *
66506 ATGAAAATTTTAT-GAAGAGGTT
1 ACCAAAATTTCATAG-AGAGGTT
* *
66528 ATCGAAAA-TACATAGAGAGG
1 A-CCAAAATTTCATAGAGAGG
66548 ATAACACAGT
Statistics
Matches: 163, Mismatches: 36, Indels: 32
0.71 0.16 0.14
Matches are distributed among these distances:
16 10 0.06
17 2 0.01
19 1 0.01
21 20 0.12
22 106 0.65
23 8 0.05
24 1 0.01
25 2 0.01
26 13 0.08
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.31
Consensus pattern (22 bp):
ACCAAAATTTCATAGAGAGGTT
Found at i:66599 original size:22 final size:23
Alignment explanation
Indices: 66565--66807 Score: 100
Period size: 22 Copynumber: 11.0 Consensus size: 23
66555 AGTTTCATTC
* * *
66565 TCATAGGGAGGTTATCGAAA-TT
1 TCATAGTGCGGTTATCAAAATTT
* *
66587 TCATGGTGTGGTTATCAAAATTT
1 TCATAGTGCGGTTATCAAAATTT
*
66610 TCATAGTGCGGTTA-C-CAATTT
1 TCATAGTGCGGTTATCAAAATTT
* * *
66631 T-ATTTAGTGTGATTATTAAAATTT
1 TCA--TAGTGCGGTTATCAAAATTT
*
66655 T-ATAG-GCAGATTATCAAAA-TT
1 TCATAGTGC-GGTTATCAAAATTT
* * * * *
66676 TCACACTGAGATTATCGAAA-TT
1 TCATAGTGCGGTTATCAAAATTT
* * *
66698 TCATAGTGTGGTTACCCAAA-TT
1 TCATAGTGCGGTTATCAAAATTT
* *
66720 TCATAGTGTGGTTATC-GAATTT
1 TCATAGTGCGGTTATCAAAATTT
*
66742 TCATAAG-GAGGTTATCAAAA-TT
1 TCAT-AGTGCGGTTATCAAAATTT
**
66764 TCATA-TTAGGTTATC-AAATTT
1 TCATAGTGCGGTTATCAAAATTT
* * * * *
66785 GCAAAATGTGGTTATCAATATTT
1 TCATAGTGCGGTTATCAAAATTT
66808 CTACACTGGA
Statistics
Matches: 173, Mismatches: 33, Indels: 29
0.74 0.14 0.12
Matches are distributed among these distances:
20 4 0.02
21 26 0.15
22 112 0.65
23 24 0.14
24 7 0.04
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.40
Consensus pattern (23 bp):
TCATAGTGCGGTTATCAAAATTT
Found at i:66755 original size:44 final size:43
Alignment explanation
Indices: 66565--66784 Score: 155
Period size: 44 Copynumber: 5.0 Consensus size: 43
66555 AGTTTCATTC
* *
66565 TCATAGGGAGGTTATCGAAATTTCATGGTGTGGTTATCAAAATTT
1 TCATA-GGAGGTTATCAAAATTTCATAGTGTGGTTATC-AAATTT
* * * * *
66610 TCATAGTGCGGTTA-C-CAATTTTATTTAGTGTGATTATTAAAATTT
1 TCATAG-GAGGTTATCAAAATTTCA--TAGTGTGGTTA-TCAAATTT
* * * * *
66655 T-ATAGGCAGATTATCAAAATTTCACACTGAGATTATCGAAA-TT
1 TCATAGG-AGGTTATCAAAATTTCATAGTGTGGTTATC-AAATTT
* * * *
66698 TCATAGTGTGGTTACCCAAATTTCATAGTGTGGTTATCGAATTT
1 TCATAG-GAGGTTATCAAAATTTCATAGTGTGGTTATCAAATTT
66742 TCATAAGGAGGTTATCAAAATTTCATA-T-TAGGTTATCAAATTT
1 TCAT-AGGAGGTTATCAAAATTTCATAGTGT-GGTTATCAAATTT
66785 GCAAAATGTG
Statistics
Matches: 135, Mismatches: 27, Indels: 28
0.71 0.14 0.15
Matches are distributed among these distances:
42 1 0.01
43 26 0.19
44 70 0.52
45 31 0.23
46 7 0.05
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.40
Consensus pattern (43 bp):
TCATAGGAGGTTATCAAAATTTCATAGTGTGGTTATCAAATTT
Found at i:66777 original size:43 final size:44
Alignment explanation
Indices: 66665--66808 Score: 132
Period size: 44 Copynumber: 3.3 Consensus size: 44
66655 TATAGGCAGA
* * * *
66665 TTATCAAAATTTCACACTGAGATTATCGAAATTTCAT-AGTGTGG
1 TTATCAAAATTTCATACTTAGGTTATCGAATTTTCATAAG-GTGG
* * * *
66709 TTACCCAAATTTCATAGTGT-GGTTATCGAATTTTCATAAGGAGG
1 TTATCAAAATTTCATACT-TAGGTTATCGAATTTTCATAAGGTGG
* * * *
66753 TTATCAAAATTTCATA-TTAGGTTATCAAATTTGCAAAATGTGG
1 TTATCAAAATTTCATACTTAGGTTATCGAATTTTCATAAGGTGG
*
66796 TTATCAATATTTC
1 TTATCAAAATTTC
66809 TACACTGGAG
Statistics
Matches: 81, Mismatches: 16, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
42 1 0.01
43 32 0.40
44 46 0.57
45 2 0.02
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.39
Consensus pattern (44 bp):
TTATCAAAATTTCATACTTAGGTTATCGAATTTTCATAAGGTGG
Done.