Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015606.1 Corchorus olitorius cultivar O-4 contig15639, 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: 67448
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1949 original size:13 final size:14
Alignment explanation
Indices: 1931--1959 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1921 TCTTTCTTCC
1931 TTCC-TTTTTTCTT
1 TTCCTTTTTTTCTT
1944 TTCCTTTTTTTCTT
1 TTCCTTTTTTTCTT
1958 TT
1 TT
1960 TTTTTCATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (14 bp):
TTCCTTTTTTTCTT
Found at i:2782 original size:19 final size:19
Alignment explanation
Indices: 2752--2794 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
2742 ATGAGTAGTT
*
2752 TTAAAGTAAAAATGTAATA
1 TTAAAGTAAAAATATAATA
2771 TATAAA-TAAAAATATAATA
1 T-TAAAGTAAAAATATAATA
2790 TTAAA
1 TTAAA
2795 ATATTTAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 4 0.18
19 14 0.64
20 4 0.18
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.33
Consensus pattern (19 bp):
TTAAAGTAAAAATATAATA
Found at i:5224 original size:65 final size:65
Alignment explanation
Indices: 5098--5224 Score: 157
Period size: 65 Copynumber: 2.0 Consensus size: 65
5088 ATATAAAAGT
* * * *
5098 AGAAAAGTATGAGGGTCATTTGATAAATAATTCAAAAAAAAAAATATTTGTTAGTGGGGATTGAA
1 AGAAAAATATGAGGGTAATTTGATAAATAATCCAAAAAAAAAAATATTTGTTAGTGAGGATTGAA
* * * * *
5163 AGAAAAATATGGGGGTAATTTGATAAATAGTCCAAATAAGAAAATGTTTGTT-GATGAGGATT
1 AGAAAAATATGAGGGTAATTTGATAAATAATCCAAAAAAAAAAATATTTGTTAG-TGAGGATT
5225 TCAAAACATA
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
64 1 0.02
65 51 0.98
ACGTcount: A:0.44, C:0.03, G:0.23, T:0.30
Consensus pattern (65 bp):
AGAAAAATATGAGGGTAATTTGATAAATAATCCAAAAAAAAAAATATTTGTTAGTGAGGATTGAA
Found at i:6097 original size:305 final size:309
Alignment explanation
Indices: 5537--6134 Score: 884
Period size: 305 Copynumber: 1.9 Consensus size: 309
5527 AACCAAAAAT
*
5537 ATAAAAATAAAAACTAACGCGTTAAGTCGTCCAACCCATAATTGTAAAGGATTAAATTGCAAAAA
1 ATAAAAATAAAAACTAACGCATTAAGTCGTCCAACCCATAATTGTAAAGG---AAATT-CAAAAA
* *
5602 GCACAAAAGTACGAGGATCATTTAATAAATAATCCAACAAAAAATATTAGTTTATGGAGAATGAG
62 GCACAAAAGTACGAGGATCATTTAATAAATAATCCAACAAAAAATATTAGTTTATGAACAATGAG
* * * * *
5667 ACACACAAATAGTAACTTTTTCACAAAGTTTCCAAAACGCCCTCAATCCTAAACGCAAATAATGA
127 ACACACAAATAGTAACTTTATCACAAAGTTCCCAAAACACCCTCAATCCTAAACCCAAATAACGA
* * *
5732 AAAAATCGAGCATGAAAGTACCAAAATACCCCTGACAACTTCTTCTTGGTTGATTGTGGTGCATC
192 AAAAATCGAGCATGAAAATACCAAAATACCCCTGACAACTTCTTCTTGGGTGAATGTGGTGCATC
* *
5797 TTATAGCTGGACAAAAGGGTAATTTCATTTCCAACTTTAATATATGTTATAGA
257 TTATAACTGGACAAAAGGGTAATTCCATTTCCAACTTTAATATATGTTATAGA
* *
5850 ATAAAAATAAAAGGC-AACGCATTAAGTCGTCCAACCCATAATTGTAAA-G-AATT-AAATAGCA
1 ATAAAAATAAAA-ACTAACGCATTAAGTCGTCCAACCCATAATTGTAAAGGAAATTCAAAAAGCA
* * * *
5911 -TAAA-TATGAGGATCATTTCATAAATAATCCAACAAAAAAATATTAGTTTATGAACAATGGGAC
65 CAAAAGTACGAGGATCATTTAATAAATAATCCAAC-AAAAAATATTAGTTTATGAACAATGAGAC
*
5974 CCACAAATAGTAACTTTATCACAAAGTTCCCAAAACACCCTCAATCCTAAACCCAAATAACGAAA
129 ACACAAATAGTAACTTTATCACAAAGTTCCCAAAACACCCTCAATCCTAAACCCAAATAACGAAA
* * * *
6039 AAATTGAGCATGAAAATACCGAAATACCCCTGACAATTTGTTCTTGGGTGAATGTGGTGCATCTT
194 AAATCGAGCATGAAAATACCAAAATACCCCTGACAACTTCTTCTTGGGTGAATGTGGTGCATCTT
6104 ATAACTGGACAAAAGGGTAATTCCATTTCCA
259 ATAACTGGACAAAAGGGTAATTCCATTTCCA
6135 TTTTCAAAAA
Statistics
Matches: 259, Mismatches: 24, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
304 27 0.10
305 175 0.68
306 7 0.03
308 4 0.02
312 1 0.00
313 44 0.17
314 1 0.00
ACGTcount: A:0.42, C:0.18, G:0.14, T:0.26
Consensus pattern (309 bp):
ATAAAAATAAAAACTAACGCATTAAGTCGTCCAACCCATAATTGTAAAGGAAATTCAAAAAGCAC
AAAAGTACGAGGATCATTTAATAAATAATCCAACAAAAAATATTAGTTTATGAACAATGAGACAC
ACAAATAGTAACTTTATCACAAAGTTCCCAAAACACCCTCAATCCTAAACCCAAATAACGAAAAA
ATCGAGCATGAAAATACCAAAATACCCCTGACAACTTCTTCTTGGGTGAATGTGGTGCATCTTAT
AACTGGACAAAAGGGTAATTCCATTTCCAACTTTAATATATGTTATAGA
Found at i:13286 original size:19 final size:19
Alignment explanation
Indices: 13262--13298 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
13252 GGTTCTTTTG
13262 ATTCTTGCTGAAGTTATTT
1 ATTCTTGCTGAAGTTATTT
13281 ATTCTTGCTGAAGTTATT
1 ATTCTTGCTGAAGTTATT
13299 CTTGCAACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.22, C:0.11, G:0.16, T:0.51
Consensus pattern (19 bp):
ATTCTTGCTGAAGTTATTT
Found at i:22586 original size:25 final size:25
Alignment explanation
Indices: 22543--22599 Score: 64
Period size: 23 Copynumber: 2.3 Consensus size: 25
22533 TGATAAATTT
*
22543 TTATATATAGTTATGATTTCTTAAAAA
1 TTATATGTAGTTATGA-TT-TTAAAAA
22570 TTATATGTA-TTAT-ATTTTAAAAA
1 TTATATGTAGTTATGATTTTAAAAA
*
22593 TAATATG
1 TTATATG
22600 GAGAAGCATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 13 0.46
24 2 0.07
25 1 0.04
26 4 0.14
27 8 0.29
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.49
Consensus pattern (25 bp):
TTATATGTAGTTATGATTTTAAAAA
Found at i:24154 original size:27 final size:27
Alignment explanation
Indices: 24114--24182 Score: 120
Period size: 27 Copynumber: 2.6 Consensus size: 27
24104 TGAGATAAAT
24114 TGGATCCTGATGGTCGGGATGCCAAGG
1 TGGATCCTGATGGTCGGGATGCCAAGG
*
24141 TTGATCCTGATGGTCGGGATGCCAAGG
1 TGGATCCTGATGGTCGGGATGCCAAGG
*
24168 TGGATCTTGATGGTC
1 TGGATCCTGATGGTC
24183 ATGAGCCGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.17, C:0.17, G:0.38, T:0.28
Consensus pattern (27 bp):
TGGATCCTGATGGTCGGGATGCCAAGG
Found at i:24200 original size:27 final size:27
Alignment explanation
Indices: 24176--24242 Score: 116
Period size: 27 Copynumber: 2.5 Consensus size: 27
24166 GGTGGATCTT
24176 GATGGTCATGAGCCGAAATAAGATCCC
1 GATGGTCATGAGCCGAAATAAGATCCC
*
24203 GATGGTCATGAGCCGAAATTAGATCCC
1 GATGGTCATGAGCCGAAATAAGATCCC
*
24230 GACGGTCATGAGC
1 GATGGTCATGAGC
24243 AATTTGGATC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.30, C:0.22, G:0.28, T:0.19
Consensus pattern (27 bp):
GATGGTCATGAGCCGAAATAAGATCCC
Found at i:30373 original size:36 final size:36
Alignment explanation
Indices: 30329--30400 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
30319 ATGAATTTAG
30329 AGATTCAAAGCTGCTCATAT-AAGGAGTGGTGCCTTT
1 AGATTCAAAGCTGCTCAT-TGAAGGAGTGGTGCCTTT
30365 AGATTCAAAGCTGCTCATTGAAGGAGTGGTGCCTTT
1 AGATTCAAAGCTGCTCATTGAAGGAGTGGTGCCTTT
30401 TCATCCCCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
35 1 0.03
36 34 0.97
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (36 bp):
AGATTCAAAGCTGCTCATTGAAGGAGTGGTGCCTTT
Found at i:30908 original size:20 final size:20
Alignment explanation
Indices: 30885--30925 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
30875 AGATATTCGA
30885 TCTATAGAGTAGATTAAATT
1 TCTATAGAGTAGATTAAATT
30905 TCTATAGAGTAGATTAAATT
1 TCTATAGAGTAGATTAAATT
30925 T
1 T
30926 TGCTTCATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.39, C:0.05, G:0.15, T:0.41
Consensus pattern (20 bp):
TCTATAGAGTAGATTAAATT
Found at i:35343 original size:20 final size:20
Alignment explanation
Indices: 35318--35356 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
35308 TTTGAATCTT
35318 TATATATCTTCATACCTCTG
1 TATATATCTTCATACCTCTG
35338 TATATATCTTCATACCTCT
1 TATATATCTTCATACCTCT
35357 TCTCTTGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.26, C:0.26, G:0.03, T:0.46
Consensus pattern (20 bp):
TATATATCTTCATACCTCTG
Found at i:36066 original size:36 final size:36
Alignment explanation
Indices: 36019--36092 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
36009 TCCTGGAGAC
36019 TCCCAATAATTAGAGCTTGGGATTTCTTCTTGAAAA
1 TCCCAATAATTAGAGCTTGGGATTTCTTCTTGAAAA
36055 TCCCAATAATTAGAGCTTGGGATTTCTTCTTGAAAA
1 TCCCAATAATTAGAGCTTGGGATTTCTTCTTGAAAA
36091 TC
1 TC
36093 TCGAGTTTGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36
Consensus pattern (36 bp):
TCCCAATAATTAGAGCTTGGGATTTCTTCTTGAAAA
Found at i:36149 original size:36 final size:36
Alignment explanation
Indices: 36102--36173 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
36092 CTCGAGTTTG
36102 GATCCTGAGATGGGCTTGCAGGGTGGGTTTATAAGA
1 GATCCTGAGATGGGCTTGCAGGGTGGGTTTATAAGA
*
36138 GATCCTGAGATGGGCTTGCGGGGTGGGTTTATAAGA
1 GATCCTGAGATGGGCTTGCAGGGTGGGTTTATAAGA
36174 CGGGGTGGGT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.21, C:0.11, G:0.40, T:0.28
Consensus pattern (36 bp):
GATCCTGAGATGGGCTTGCAGGGTGGGTTTATAAGA
Found at i:36179 original size:18 final size:18
Alignment explanation
Indices: 36156--36194 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
36146 GATGGGCTTG
36156 CGGGGTGGGTTTATAAGA
1 CGGGGTGGGTTTATAAGA
36174 CGGGGTGGGTTTATAAGA
1 CGGGGTGGGTTTATAAGA
36192 CGG
1 CGG
36195 AAGAGGGTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.21, C:0.08, G:0.46, T:0.26
Consensus pattern (18 bp):
CGGGGTGGGTTTATAAGA
Found at i:36205 original size:18 final size:18
Alignment explanation
Indices: 36162--36203 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
36152 CTTGCGGGGT
* *
36162 GGGTTTATAAGACGGGGT
1 GGGTTTATAAGACGGAGA
36180 GGGTTTATAAGACGGAAGA
1 GGGTTTATAAGACGG-AGA
36199 GGGTT
1 GGGTT
36204 ATTTTTTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.26, C:0.05, G:0.43, T:0.26
Consensus pattern (18 bp):
GGGTTTATAAGACGGAGA
Found at i:36604 original size:68 final size:68
Alignment explanation
Indices: 36495--36632 Score: 276
Period size: 68 Copynumber: 2.0 Consensus size: 68
36485 AAAAAACAGA
36495 GTCTACCCAAAAAAAATGTAGTAGCTCAATTGAATTGTAAAAAGGGCAATGGAATCATTTACAAG
1 GTCTACCCAAAAAAAATGTAGTAGCTCAATTGAATTGTAAAAAGGGCAATGGAATCATTTACAAG
36560 GAC
66 GAC
36563 GTCTACCCAAAAAAAATGTAGTAGCTCAATTGAATTGTAAAAAGGGCAATGGAATCATTTACAAG
1 GTCTACCCAAAAAAAATGTAGTAGCTCAATTGAATTGTAAAAAGGGCAATGGAATCATTTACAAG
36628 GAC
66 GAC
36631 GT
1 GT
36633 AATGTAACTA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 70 1.00
ACGTcount: A:0.42, C:0.14, G:0.20, T:0.24
Consensus pattern (68 bp):
GTCTACCCAAAAAAAATGTAGTAGCTCAATTGAATTGTAAAAAGGGCAATGGAATCATTTACAAG
GAC
Found at i:39234 original size:11 final size:12
Alignment explanation
Indices: 39215--39252 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
39205 TTATGACTTG
*
39215 TATATATATGTT
1 TATATATATGTA
39227 TA-ATATATGTA
1 TATATATATGTA
*
39238 TATATATATATA
1 TATATATATGTA
39250 TAT
1 TAT
39253 TTACAAGTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 10 0.43
12 13 0.57
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (12 bp):
TATATATATGTA
Found at i:47765 original size:76 final size:73
Alignment explanation
Indices: 47635--47780 Score: 238
Period size: 76 Copynumber: 2.0 Consensus size: 73
47625 TAATTAAGTT
*
47635 CATTAATGGAAAATTGAATTTCTCTTTTAGCTAAGATGAATGCAGTCGAGGGAAAAAAATTGAAT
1 CATTAATGGAAAATTGAATTTCTCTTTTAGCTAAGATGAATGCACTCGAGGG---AAAATTGAAT
47700 TTCCCTAGTAA
63 TTCCCTAGTAA
* *
47711 CATTAATGGAAAATTGAATTTCTCTTTTAGCTAAGATGAATTCACTCGATGGAAAATTGAATTTC
1 CATTAATGGAAAATTGAATTTCTCTTTTAGCTAAGATGAATGCACTCGAGGGAAAATTGAATTTC
47776 CCTAG
66 CCTAG
47781 ATAGTTCGAA
Statistics
Matches: 67, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
73 18 0.27
76 49 0.73
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34
Consensus pattern (73 bp):
CATTAATGGAAAATTGAATTTCTCTTTTAGCTAAGATGAATGCACTCGAGGGAAAATTGAATTTC
CCTAGTAA
Found at i:49648 original size:15 final size:15
Alignment explanation
Indices: 49630--49658 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
49620 TCTTTTTTGT
49630 TTAGTCCTTTACTAC
1 TTAGTCCTTTACTAC
49645 TTAGTCCTTTACTA
1 TTAGTCCTTTACTA
49659 ATTCTATCTT
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:0.21, C:0.24, G:0.07, T:0.48
Consensus pattern (15 bp):
TTAGTCCTTTACTAC
Found at i:49690 original size:78 final size:78
Alignment explanation
Indices: 49561--49710 Score: 282
Period size: 78 Copynumber: 1.9 Consensus size: 78
49551 TTCTACTTTA
49561 TACTACTTAGTCCTTTACTAATTCTATCGTAATCGATTCAACGCTTCAGCTTTATTATTTCTTTT
1 TACTACTTAGTCCTTTACTAATTCTATCGTAATCGATTCAACGCTTCAGCTTTATTATTTCTTTT
49626 TTGTTTAGTCCTT
66 TTGTTTAGTCCTT
* *
49639 TACTACTTAGTCCTTTACTAATTCTATCTTAATCGATTCAACGCTTCAGCTTTATTTTTTCTTTT
1 TACTACTTAGTCCTTTACTAATTCTATCGTAATCGATTCAACGCTTCAGCTTTATTATTTCTTTT
49704 TTGTTTA
66 TTGTTTA
49711 TTTGTCCGAT
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
78 70 1.00
ACGTcount: A:0.21, C:0.20, G:0.08, T:0.51
Consensus pattern (78 bp):
TACTACTTAGTCCTTTACTAATTCTATCGTAATCGATTCAACGCTTCAGCTTTATTATTTCTTTT
TTGTTTAGTCCTT
Found at i:55882 original size:60 final size:62
Alignment explanation
Indices: 55770--55885 Score: 164
Period size: 60 Copynumber: 1.9 Consensus size: 62
55760 TTGTTCTTGG
* *
55770 ATTAATATACTTAAATCTTTTAGATTAGTTTTTCAGTCATTTCACTTGCTCTTCTTGAATTA
1 ATTAATATACTTAAATCTTTGAGATTAGTTTTTCAGTCATTTCACTTCCTCTTCTTGAATTA
* * **
55832 ATTAATGTGCTTAAATC-TTGAGATTA-TTTTTTTGTCATTTCACTTCCTCTTCTT
1 ATTAATATACTTAAATCTTTGAGATTAGTTTTTCAGTCATTTCACTTCCTCTTCTT
55886 ATTGTTTTGT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
60 25 0.52
61 8 0.17
62 15 0.31
ACGTcount: A:0.24, C:0.16, G:0.09, T:0.52
Consensus pattern (62 bp):
ATTAATATACTTAAATCTTTGAGATTAGTTTTTCAGTCATTTCACTTCCTCTTCTTGAATTA
Found at i:60683 original size:21 final size:21
Alignment explanation
Indices: 60659--60725 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
60649 AATTCTCTAT
60659 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
* * ***
60680 AAATCATAAAAAATTCT-TTGT-
1 AAAT--TAAGAAATACTCAACTC
60701 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
60722 AAAT
1 AAAT
60726 CTCAAATCCT
Statistics
Matches: 32, Mismatches: 10, Indels: 8
0.64 0.20 0.16
Matches are distributed among these distances:
19 9 0.28
20 1 0.03
21 12 0.38
22 1 0.03
23 9 0.28
ACGTcount: A:0.52, C:0.15, G:0.04, T:0.28
Consensus pattern (21 bp):
AAATTAAGAAATACTCAACTC
Found at i:60706 original size:42 final size:42
Alignment explanation
Indices: 60647--60726 Score: 142
Period size: 42 Copynumber: 1.9 Consensus size: 42
60637 CTAAGTCTTG
60647 AAAATTCTCTATAAATTAAGAAATACTCAACTCAAATCATAA
1 AAAATTCTCTATAAATTAAGAAATACTCAACTCAAATCATAA
* *
60689 AAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATC
1 AAAATTCTCTATAAATTAAGAAATACTCAACTCAAATC
60727 TCAAATCCTG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.50, C:0.16, G:0.04, T:0.30
Consensus pattern (42 bp):
AAAATTCTCTATAAATTAAGAAATACTCAACTCAAATCATAA
Found at i:60896 original size:55 final size:56
Alignment explanation
Indices: 60799--60911 Score: 201
Period size: 55 Copynumber: 2.0 Consensus size: 56
60789 TTTATTTTGT
*
60799 AGAATAATTAAGTAGAGATATGGGGATAAGATTTATTGTAACATTTATTGTGTGAA
1 AGAATAATTAAGTAGAGATATGGGGATAAGATTTATTATAACATTTATTGTGTGAA
*
60855 AGAATAATTAAGTAGAGATA-GGGGATATGATTTATTATAACATTTATTGTGTGAA
1 AGAATAATTAAGTAGAGATATGGGGATAAGATTTATTATAACATTTATTGTGTGAA
60910 AG
1 AG
60912 GAAACGAATA
Statistics
Matches: 55, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
55 35 0.64
56 20 0.36
ACGTcount: A:0.40, C:0.02, G:0.23, T:0.35
Consensus pattern (56 bp):
AGAATAATTAAGTAGAGATATGGGGATAAGATTTATTATAACATTTATTGTGTGAA
Found at i:61104 original size:2 final size:2
Alignment explanation
Indices: 61097--61143 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
61087 TAATATGTAG
61097 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
61139 CA TA T
1 TA TA T
61144 GTAACCCTCT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:62783 original size:10 final size:10
Alignment explanation
Indices: 62764--62799 Score: 63
Period size: 10 Copynumber: 3.6 Consensus size: 10
62754 ATACCTCGAT
62764 ATATCCGTAA
1 ATATCCGTAA
*
62774 ATATCTGTAA
1 ATATCCGTAA
62784 ATATCCGTAA
1 ATATCCGTAA
62794 ATATCC
1 ATATCC
62800 ATATTAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.39, C:0.19, G:0.08, T:0.33
Consensus pattern (10 bp):
ATATCCGTAA
Found at i:63640 original size:36 final size:35
Alignment explanation
Indices: 63512--63720 Score: 183
Period size: 36 Copynumber: 5.8 Consensus size: 35
63502 AAATGCCTTT
* * * *
63512 TGATGGGAACTTTCCCACTTTGAAAACTAAAACTGAAAA
1 TGATGGGAACTTTTCCAATTTGAAAACT-TAA---AAAC
* * * *
63551 TGACGGGAACTTTCCCTAAATTGAAAAC-TAAAACC
1 TGATGGGAACTTTTCC-AATTTGAAAACTTAAAAAC
*
63586 TGATGCGAA-TTTTCCCAATTT-AAAACTTTAAAAAC
1 TGATGGGAACTTTT-CCAATTTGAAAAC-TTAAAAAC
*
63621 TGAATGGGAACTTTTCCAATTTAAAAACTTAAAAAC
1 TG-ATGGGAACTTTTCCAATTTGAAAACTTAAAAAC
* *
63657 TGGTTGGGAACTTTTCCAATTTGAAAAC-TAAAACC
1 T-GATGGGAACTTTTCCAATTTGAAAACTTAAAAAC
* *
63692 TGGTGGGAACTTTCCCAATTTGAAAACTT
1 TGATGGGAACTTTTCCAATTTGAAAACTT
63721 CGAAGACTGA
Statistics
Matches: 144, Mismatches: 17, Indels: 22
0.79 0.09 0.12
Matches are distributed among these distances:
33 5 0.03
34 31 0.22
35 27 0.19
36 45 0.31
37 10 0.07
38 2 0.01
39 15 0.10
40 9 0.06
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.30
Consensus pattern (35 bp):
TGATGGGAACTTTTCCAATTTGAAAACTTAAAAAC
Found at i:67116 original size:13 final size:14
Alignment explanation
Indices: 67079--67117 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
67069 GCTTTTAAAG
*
67079 GATTTTTCAAAAAT
1 GATTTCTCAAAAAT
67093 GATTTCTCAAAAAT
1 GATTTCTCAAAAAT
*
67107 GGTTTC-CAAAA
1 GATTTCTCAAAA
67118 TTTGTTTTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 5 0.22
14 18 0.78
ACGTcount: A:0.41, C:0.13, G:0.10, T:0.36
Consensus pattern (14 bp):
GATTTCTCAAAAAT
Done.