Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006883.1 Corchorus capsularis cultivar CVL-1 contig06904, 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: 45904
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.32
Found at i:1569 original size:22 final size:24
Alignment explanation
Indices: 1534--1579 Score: 78
Period size: 22 Copynumber: 2.0 Consensus size: 24
1524 GGTAGTAATC
1534 AGTGAATCGATAATTAAGAGTTAA
1 AGTGAATCGATAATTAAGAGTTAA
1558 AGTG-ATC-ATAATTAAGAGTTAA
1 AGTGAATCGATAATTAAGAGTTAA
1580 GTGGTTAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 15 0.68
23 3 0.14
24 4 0.18
ACGTcount: A:0.46, C:0.04, G:0.20, T:0.30
Consensus pattern (24 bp):
AGTGAATCGATAATTAAGAGTTAA
Found at i:1786 original size:22 final size:22
Alignment explanation
Indices: 1761--1813 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
1751 AAGGTATCTA
* * *
1761 AAAGGGTAAAATGGTAATTAGT
1 AAAGAGTAAAATAGTAATCAGT
1783 AAAGAGTAAAATAGTAATCAGT
1 AAAGAGTAAAATAGTAATCAGT
*
1805 AAAAAGTAA
1 AAAGAGTAA
1814 GAAGGTAGTC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.55, C:0.02, G:0.21, T:0.23
Consensus pattern (22 bp):
AAAGAGTAAAATAGTAATCAGT
Found at i:1907 original size:21 final size:21
Alignment explanation
Indices: 1881--1992 Score: 66
Period size: 22 Copynumber: 5.2 Consensus size: 21
1871 AAGGGTAATA
*
1881 AGTAAGAAGCAAAAGGAAATT
1 AGTAAGAAGCAAAAGGAAATC
* *
1902 AGTAAG-AGTAAAAAGGTAATC
1 AGTAAGAAG-CAAAAGGAAATC
* **
1923 AGTAAAAAGCAAAAAGCTAATC
1 AGTAAGAAGC-AAAAGGAAATC
* * * *
1945 AGCAAAAAGTAAAAAGGTAATC
1 AGTAAGAAG-CAAAAGGAAATC
* *
1967 -GATAAAAAGCAAAAGGCAATC
1 AG-TAAGAAGCAAAAGGAAATC
1988 AGTAA
1 AGTAA
1993 AAACTAAAAA
Statistics
Matches: 73, Mismatches: 12, Indels: 12
0.75 0.12 0.12
Matches are distributed among these distances:
20 2 0.03
21 34 0.47
22 37 0.51
ACGTcount: A:0.57, C:0.09, G:0.20, T:0.14
Consensus pattern (21 bp):
AGTAAGAAGCAAAAGGAAATC
Found at i:1938 original size:43 final size:42
Alignment explanation
Indices: 1857--2088 Score: 164
Period size: 43 Copynumber: 5.2 Consensus size: 42
1847 TAAATAGTAC
* * *
1857 TCAGTAAGAGTAAAAAGGGTAATAAGTAAGAAGCAAAAGGAAA
1 TCAGTAAAAGTAAAAA-GGTAATCAGTAAAAAGCAAAAGGAAA
* * **
1900 TTAGTAAGAGTAAAAAGGTAATCAGTAAAAAGCAAAAAGCTAA
1 TCAGTAAAAGTAAAAAGGTAATCAGTAAAAAGC-AAAAGGAAA
* *
1943 TCAGCAAAAAGTAAAAAGGTAATC-GATAAAAAGCAAAAGGCAA
1 TCAG-TAAAAGTAAAAAGGTAATCAG-TAAAAAGCAAAAGGAAA
* * *
1986 TCAGTAAAAACTAAAAA-GTAACCAGTAAAAAAGGGAGCAGAAAATGGTAA
1 TCAGT-AAAAGTAAAAAGGTAATCAGT--AAAA---AGC--AAAA-GGAAA
* * *
2036 TCAGAAAAAGAGTAAAATGGTAATCAGTAAAAAGTAAAA-GATAA
1 TCAG-TAAA-AGTAAAAAGGTAATCAGTAAAAAGCAAAAGGA-AA
2080 TCAGTAAAA
1 TCAGTAAAA
2089 TAGTAATCAG
Statistics
Matches: 151, Mismatches: 21, Indels: 35
0.73 0.10 0.17
Matches are distributed among these distances:
42 22 0.15
43 52 0.34
44 35 0.23
45 4 0.03
47 5 0.03
49 4 0.03
50 15 0.10
51 6 0.04
52 8 0.05
ACGTcount: A:0.57, C:0.08, G:0.20, T:0.16
Consensus pattern (42 bp):
TCAGTAAAAGTAAAAAGGTAATCAGTAAAAAGCAAAAGGAAA
Found at i:1943 original size:22 final size:22
Alignment explanation
Indices: 1868--2088 Score: 150
Period size: 21 Copynumber: 9.9 Consensus size: 22
1858 CAGTAAGAGT
* *
1868 AAAAAGGGTAATAAGTAAGAAGC
1 AAAAA-GGTAATCAGTAAAAAGC
* * * *
1891 -AAAAGGAAATTAGT-AAGAGT
1 AAAAAGGTAATCAGTAAAAAGC
1911 AAAAAGGTAATCAGTAAAAAGC
1 AAAAAGGTAATCAGTAAAAAGC
* * *
1933 AAAAAGCTAATCAGCAAAAAGT
1 AAAAAGGTAATCAGTAAAAAGC
1955 AAAAAGGTAATC-GATAAAAAGC
1 AAAAAGGTAATCAG-TAAAAAGC
*
1977 -AAAAGGCAATCAGTAAAAA-C
1 AAAAAGGTAATCAGTAAAAAGC
*
1997 TAAAAA-GTAACCAGTAAAAAAGGGAGC
1 -AAAAAGGTAATCAGT--AAAA---AGC
* *
2024 AGAAAATGGTAATCAGAAAAAGAGT
1 A-AAAA-GGTAATCAGTAAAA-AGC
*
2049 AAAATGGTAATCAGTAAAAAG-
1 AAAAAGGTAATCAGTAAAAAGC
* *
2070 TAAAAGATAATCAGTAAAA
1 AAAAAGGTAATCAGTAAAA
2089 TAGTAATCAG
Statistics
Matches: 157, Mismatches: 26, Indels: 32
0.73 0.12 0.15
Matches are distributed among these distances:
20 4 0.03
21 60 0.38
22 51 0.32
23 17 0.11
24 3 0.02
25 4 0.03
26 2 0.01
27 9 0.06
29 7 0.04
ACGTcount: A:0.58, C:0.08, G:0.19, T:0.15
Consensus pattern (22 bp):
AAAAAGGTAATCAGTAAAAAGC
Found at i:1964 original size:44 final size:44
Alignment explanation
Indices: 1857--2094 Score: 184
Period size: 44 Copynumber: 5.3 Consensus size: 44
1847 TAAATAGTAC
* * * **
1857 TCAGT-AAGAGTAAAAAGGGTAATAAGTAAGAAGC-AAAAGGAAA
1 TCAGTAAAAAGTAAAAA-GGTAATCAGTAAAAAGCAAAAAGCTAA
* *
1900 TTAGT-AAGAGTAAAAAGGTAATCAGTAAAAAGCAAAAAGCTAA
1 TCAGTAAAAAGTAAAAAGGTAATCAGTAAAAAGCAAAAAGCTAA
* *
1943 TCAGCAAAAAGTAAAAAGGTAATC-GATAAAAAGCAAAAGGC-AA
1 TCAGTAAAAAGTAAAAAGGTAATCAG-TAAAAAGCAAAAAGCTAA
* * *
1986 TCAGTAAAAACTAAAAA-GTAACCAGTAAAAAAGGGAGCAGAAAATGGTAA
1 TCAGTAAAAAGTAAAAAGGTAATCAGT--AAAA---AGCA-AAAA-GCTAA
* * * *
2036 TCAGAAAAAGAGTAAAATGGTAATCAGTAAAAAG-TAAAAGATAA
1 TCAGTAAAA-AGTAAAAAGGTAATCAGTAAAAAGCAAAAAGCTAA
2080 TCAGTAAAATAGTAA
1 TCAGTAAAA-AGTAA
2095 TCAGTAAAAG
Statistics
Matches: 159, Mismatches: 22, Indels: 27
0.76 0.11 0.13
Matches are distributed among these distances:
42 21 0.13
43 44 0.28
44 52 0.33
45 4 0.03
47 6 0.04
48 3 0.02
49 1 0.01
50 14 0.09
51 6 0.04
52 8 0.05
ACGTcount: A:0.57, C:0.08, G:0.20, T:0.16
Consensus pattern (44 bp):
TCAGTAAAAAGTAAAAAGGTAATCAGTAAAAAGCAAAAAGCTAA
Found at i:2085 original size:14 final size:14
Alignment explanation
Indices: 2068--2115 Score: 69
Period size: 14 Copynumber: 3.4 Consensus size: 14
2058 ATCAGTAAAA
2068 AGTAAAAGATAATC
1 AGTAAAAGATAATC
*
2082 AGTAAAATAGTAATC
1 AGTAAAAGA-TAATC
*
2097 AGTAAAAGGTAATC
1 AGTAAAAGATAATC
2111 AGTAA
1 AGTAA
2116 GAGTAAAACA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
14 18 0.60
15 12 0.40
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (14 bp):
AGTAAAAGATAATC
Found at i:2108 original size:73 final size:71
Alignment explanation
Indices: 1956--2112 Score: 176
Period size: 73 Copynumber: 2.2 Consensus size: 71
1946 GCAAAAAGTA
1956 AAAAGGTAATC-GATAAAAAGCAAAAGGCAATCAGTAAAAACTAAAAAGTAACCAGTAAAAAAGG
1 AAAAGGTAATCAGATAAAAAGCAAAAGGCAATCAGTAAAAACTAAAAAGTAACCAGTAAAAAAGG
*
2020 GAGCAG
66 AAGCAG
* * * *
2026 AAAATGGTAATCAGA-AAAAGAGTAAAATGGTAATCAGTAAAAAGT-AAAAGATAATCAGTAAAA
1 AAAA-GGTAATCAGATAAAA-AGCAAAA-GGCAATCAGTAAAAACTAAAAAG-TAACCAGTAAAA
* * *
2089 TAGTAATCAG
62 AAGGAAGCAG
2099 TAAAAGGTAATCAG
1 -AAAAGGTAATCAG
2113 TAAGAGTAAA
Statistics
Matches: 73, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
70 4 0.05
71 11 0.15
72 13 0.18
73 41 0.56
74 4 0.05
ACGTcount: A:0.56, C:0.08, G:0.19, T:0.17
Consensus pattern (71 bp):
AAAAGGTAATCAGATAAAAAGCAAAAGGCAATCAGTAAAAACTAAAAAGTAACCAGTAAAAAAGG
AAGCAG
Found at i:2261 original size:29 final size:28
Alignment explanation
Indices: 2236--2291 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 28
2226 GTAAAAAGTG
2236 GTAATAAATAAAAGAGAGTAAGAAAAGA
1 GTAATAAATAAAAGAGAGTAAGAAAAGA
***
2264 GTAATTGGTAAAA-AGAGTAAGAAAAGA
1 GTAATAAATAAAAGAGAGTAAGAAAAGA
2291 G
1 G
2292 AGAAAAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 15 0.60
28 10 0.40
ACGTcount: A:0.59, C:0.00, G:0.25, T:0.16
Consensus pattern (28 bp):
GTAATAAATAAAAGAGAGTAAGAAAAGA
Found at i:3156 original size:15 final size:16
Alignment explanation
Indices: 3124--3157 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
3114 AAAGAAGATT
*
3124 TAAAATTAAATCTAAC
1 TAAAAGTAAATCTAAC
3140 TAAAAGTAAAT-TAAC
1 TAAAAGTAAATCTAAC
3155 TAA
1 TAA
3158 GAAAACAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.59, C:0.09, G:0.03, T:0.29
Consensus pattern (16 bp):
TAAAAGTAAATCTAAC
Found at i:13148 original size:17 final size:17
Alignment explanation
Indices: 13122--13186 Score: 76
Period size: 17 Copynumber: 3.8 Consensus size: 17
13112 CCCCTCATGG
* *
13122 TACCAGGTAGTATGATA
1 TACCAGGTAGCATGAGA
*
13139 TACTAGGTAGCATGAGA
1 TACCAGGTAGCATGAGA
* *
13156 TACCAGGTAGCAAGAGG
1 TACCAGGTAGCATGAGA
*
13173 TACCAAGTAGCATG
1 TACCAGGTAGCATG
13187 TCTGACAACT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 40 1.00
ACGTcount: A:0.35, C:0.15, G:0.28, T:0.22
Consensus pattern (17 bp):
TACCAGGTAGCATGAGA
Found at i:15128 original size:2 final size:2
Alignment explanation
Indices: 15121--15152 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
15111 TGGGTTCAAC
*
15121 AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15153 CTAAAGTCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15384 original size:66 final size:66
Alignment explanation
Indices: 15284--15407 Score: 194
Period size: 66 Copynumber: 1.9 Consensus size: 66
15274 TGTTTCTACA
* * *
15284 TCATCGTAGGTTTCGATCCGTCAATCTCTACTTAGTAAGGGATTTTCAAATGACTTTAGTGTTTC
1 TCATCGCAGGTTTCGATCCGCCAATCTCTACTTAGTAAGCGATTTTCAAATGACTTTAGTGTTTC
15349 T
66 T
* * *
15350 TCATCGCAGGTTTCGATCCGCCCATCTCTGCTTAGTAAGCGATTTTCAAGTGACTTTA
1 TCATCGCAGGTTTCGATCCGCCAATCTCTACTTAGTAAGCGATTTTCAAATGACTTTA
15408 AGATACTAAT
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
66 52 1.00
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.38
Consensus pattern (66 bp):
TCATCGCAGGTTTCGATCCGCCAATCTCTACTTAGTAAGCGATTTTCAAATGACTTTAGTGTTTC
T
Found at i:16082 original size:2 final size:2
Alignment explanation
Indices: 16075--16108 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
16065 ACCCTTGATT
16075 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
16109 CTAGTTTTAG
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:16673 original size:22 final size:22
Alignment explanation
Indices: 16647--16688 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
16637 CTTGCTTTAG
*
16647 TTCCGGTGATTTGAGGGTTTGC
1 TTCCGGTGATTCGAGGGTTTGC
*
16669 TTCCGGTGGTTCGAGGGTTT
1 TTCCGGTGATTCGAGGGTTT
16689 ATTTGACGGT
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:0.07, C:0.14, G:0.38, T:0.40
Consensus pattern (22 bp):
TTCCGGTGATTCGAGGGTTTGC
Found at i:16910 original size:86 final size:85
Alignment explanation
Indices: 16801--16967 Score: 235
Period size: 85 Copynumber: 2.0 Consensus size: 85
16791 GTTTGATTTT
* * * *
16801 TTTGGGTTCGAATGAAGTTAATCTGTTGTTTATTTGCCCAAATTCTTTGATTCAATGCTTTGATT
1 TTTGGGTTCGAATCAAGTAAATCTGCTGTTTATTTG-CCAAATTCTTTCATTCAATGCTTTGATT
* *
16866 TACTGTACTTTTGTTTGTATG
65 CACTGTACTTTTCTTTGTATG
* * *
16887 TTTGGTTTCGAATCAAGTAAATCTGCTGTTTATTTGCCTAATTGTTTCATTCAATGCTTTGATTC
1 TTTGGGTTCGAATCAAGTAAATCTGCTGTTTATTTGCCAAATTCTTTCATTCAATGCTTTGATTC
*
16952 ACTGTATTTTTCTTTG
66 ACTGTACTTTTCTTTG
16968 AGATGATGGG
Statistics
Matches: 71, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
85 39 0.55
86 32 0.45
ACGTcount: A:0.20, C:0.13, G:0.17, T:0.50
Consensus pattern (85 bp):
TTTGGGTTCGAATCAAGTAAATCTGCTGTTTATTTGCCAAATTCTTTCATTCAATGCTTTGATTC
ACTGTACTTTTCTTTGTATG
Found at i:17797 original size:16 final size:17
Alignment explanation
Indices: 17766--17800 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
17756 CAAAGTTATC
17766 TAACTTAGAAACAATGT
1 TAACTTAGAAACAATGT
*
17783 TAACTT-GAGACAATGT
1 TAACTTAGAAACAATGT
17799 TA
1 TA
17801 TTGTTTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.31
Consensus pattern (17 bp):
TAACTTAGAAACAATGT
Found at i:17857 original size:51 final size:50
Alignment explanation
Indices: 17769--17869 Score: 139
Period size: 51 Copynumber: 2.0 Consensus size: 50
17759 AGTTATCTAA
* * * *
17769 CTTAGAAACAATGTTAACTTGAGACAATGTTATTGTTTATTATTGGTTTTG
1 CTTAAAAACAATGTTAACTTGAGACAATGTCACTGTTT-TTATTGATTTTG
* *
17820 CTTAAAAACAATGTTAATTTGAGACTATGTCACTGTTTTTATTGATTTTG
1 CTTAAAAACAATGTTAACTTGAGACAATGTCACTGTTTTTATTGATTTTG
17870 TTTTACTTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
50 11 0.25
51 33 0.75
ACGTcount: A:0.30, C:0.09, G:0.16, T:0.46
Consensus pattern (50 bp):
CTTAAAAACAATGTTAACTTGAGACAATGTCACTGTTTTTATTGATTTTG
Found at i:19091 original size:22 final size:22
Alignment explanation
Indices: 19035--19148 Score: 88
Period size: 22 Copynumber: 5.2 Consensus size: 22
19025 GTCCCAAGCT
* * *
19035 ATAACCACATTATGAAATTGTG
1 ATAATCACACTATGAAATTTTG
19057 ATAATCACACTATGAAATTTTG
1 ATAATCACACTATGAAATTTTG
* *
19079 ATAA-CATCCCTATTAAATTTTG
1 ATAATCA-CACTATGAAATTTTG
* * * * *
19101 AGAATAATACTATGTAATTTCG
1 ATAATCACACTATGAAATTTTG
* *
19123 AAAACCA-ATCTATGAAATTTTG
1 ATAATCACA-CTATGAAATTTTG
19145 ATAA
1 ATAA
19149 ATCTTCCTAT
Statistics
Matches: 71, Mismatches: 18, Indels: 6
0.75 0.19 0.06
Matches are distributed among these distances:
21 3 0.04
22 67 0.94
23 1 0.01
ACGTcount: A:0.42, C:0.13, G:0.10, T:0.35
Consensus pattern (22 bp):
ATAATCACACTATGAAATTTTG
Found at i:19342 original size:22 final size:23
Alignment explanation
Indices: 19308--19368 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
19298 CTAAACTACG
* *
19308 AAATTTCATTAACCTCTC-TATA
1 AAATTTTAATAACCTCTCATATA
* *
19330 AAATTTTGATAACCT-TCATATG
1 AAATTTTAATAACCTCTCATATA
*
19352 AAATTTTAATAATCTCT
1 AAATTTTAATAACCTCT
19369 TTCTGAAATT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
21 2 0.06
22 28 0.90
23 1 0.03
ACGTcount: A:0.38, C:0.16, G:0.03, T:0.43
Consensus pattern (23 bp):
AAATTTTAATAACCTCTCATATA
Found at i:20682 original size:23 final size:24
Alignment explanation
Indices: 20638--20683 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
20628 ATGGCATAAT
* *
20638 TAAAATATATATTTTGATAATGGC
1 TAAAATATATATTTTAAAAATGGC
*
20662 TAAAA-ATATGTTTTAAAAATGG
1 TAAAATATATATTTTAAAAATGG
20684 GGTACAATAG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.46, C:0.02, G:0.13, T:0.39
Consensus pattern (24 bp):
TAAAATATATATTTTAAAAATGGC
Found at i:20733 original size:2 final size:2
Alignment explanation
Indices: 20726--20772 Score: 67
Period size: 2 Copynumber: 23.0 Consensus size: 2
20716 TACGTACTTT
* *
20726 TA TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA GTA TA GA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
20769 TA TA
1 TA TA
20773 GATAAGTCAA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
2 38 0.95
3 2 0.05
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (2 bp):
TA
Found at i:21045 original size:2 final size:2
Alignment explanation
Indices: 21038--21070 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
21028 CCCTTAGTTT
21038 TA 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 TA T
21071 CGTAATTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:24137 original size:17 final size:17
Alignment explanation
Indices: 24091--24145 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 17
24081 AACCCATGTA
* * *
24091 ATCTTTGATCACCGGTA
1 ATCTTAGATCACTGGTG
*
24108 ATCTTACATCACTGGTG
1 ATCTTAGATCACTGGTG
*
24125 ATCTTAGATCACTAGTG
1 ATCTTAGATCACTGGTG
24142 ATCT
1 ATCT
24146 GGGGGGTGAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.36
Consensus pattern (17 bp):
ATCTTAGATCACTGGTG
Found at i:27920 original size:92 final size:92
Alignment explanation
Indices: 27811--27988 Score: 338
Period size: 92 Copynumber: 1.9 Consensus size: 92
27801 TTGTCTTGAA
* *
27811 GACCTAAAAACACAAATACTTCTAAAATAGGGTTAAAATACACATAAAAATAGCAAAAAGCATAG
1 GACCTAAAAACAAAAATACTTATAAAATAGGGTTAAAATACACATAAAAATAGCAAAAAGCATAG
27876 GAAAATAGCTATAAAAATAGGCTTCAT
66 GAAAATAGCTATAAAAATAGGCTTCAT
27903 GACCTAAAAACAAAAATACTTATAAAATAGGGTTAAAATACACATAAAAATAGCAAAAAGCATAG
1 GACCTAAAAACAAAAATACTTATAAAATAGGGTTAAAATACACATAAAAATAGCAAAAAGCATAG
27968 GAAAATAGCTATAAAAATAGG
66 GAAAATAGCTATAAAAATAGG
27989 ATTAATTTTA
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
92 84 1.00
ACGTcount: A:0.56, C:0.12, G:0.12, T:0.20
Consensus pattern (92 bp):
GACCTAAAAACAAAAATACTTATAAAATAGGGTTAAAATACACATAAAAATAGCAAAAAGCATAG
GAAAATAGCTATAAAAATAGGCTTCAT
Found at i:33607 original size:13 final size:13
Alignment explanation
Indices: 33589--33615 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
33579 TAATTATTTT
33589 AGGGGCTGCCGGA
1 AGGGGCTGCCGGA
33602 AGGGGCTGCCGGA
1 AGGGGCTGCCGGA
33615 A
1 A
33616 TCTGGAACTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.19, C:0.22, G:0.52, T:0.07
Consensus pattern (13 bp):
AGGGGCTGCCGGA
Found at i:38584 original size:2 final size:2
Alignment explanation
Indices: 38577--38601 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
38567 TTGAAATGTA
38577 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
38602 ATATATAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:40726 original size:36 final size:34
Alignment explanation
Indices: 40679--40749 Score: 97
Period size: 36 Copynumber: 2.0 Consensus size: 34
40669 CACTTGGGCT
*
40679 AGGCCTGGCGCGGGCCAGCTATGGCCCAGCGCCC
1 AGGCCTGGCGCGGGCCAGCCATGGCCCAGCGCCC
* *
40713 AGGCCATGTGCGCGGGCCATCCATGGCCCAGTGCCC
1 AGGCC-TG-GCGCGGGCCAGCCATGGCCCAGCGCCC
40749 A
1 A
40750 AGCTTGGGCC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
34 5 0.16
35 2 0.06
36 25 0.78
ACGTcount: A:0.14, C:0.39, G:0.35, T:0.11
Consensus pattern (34 bp):
AGGCCTGGCGCGGGCCAGCCATGGCCCAGCGCCC
Found at i:40875 original size:18 final size:18
Alignment explanation
Indices: 40832--40877 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
40822 AAGAAAAAAA
40832 AAGGAAA-AAGAGAGAAT
1 AAGGAAATAAGAGAGAAT
40849 AAGGAAAATAAG-GAGAAAT
1 AAGG-AAATAAGAGAG-AAT
40868 AAGGAAATAA
1 AAGGAAATAA
40878 AAAAAAGGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 4 0.15
18 12 0.46
19 10 0.38
ACGTcount: A:0.65, C:0.00, G:0.26, T:0.09
Consensus pattern (18 bp):
AAGGAAATAAGAGAGAAT
Found at i:43600 original size:17 final size:18
Alignment explanation
Indices: 43572--43608 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
43562 CCTCCCCATA
43572 GTACCTAGGTAGTATGAG
1 GTACCTAGGTAGTATGAG
43590 GTACC-AGGTAGTATGAG
1 GTACCTAGGTAGTATGAG
43607 GT
1 GT
43609 GATAGGTTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.27, C:0.11, G:0.35, T:0.27
Consensus pattern (18 bp):
GTACCTAGGTAGTATGAG
Found at i:44867 original size:14 final size:14
Alignment explanation
Indices: 44848--44880 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
44838 GTCTTGATTT
44848 AAATAA-AACTACAA
1 AAATAATAA-TACAA
44862 AAATAATAATACAA
1 AAATAATAATACAA
44876 AAATA
1 AAATA
44881 TAGCAATAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 16 0.89
15 2 0.11
ACGTcount: A:0.73, C:0.09, G:0.00, T:0.18
Consensus pattern (14 bp):
AAATAATAATACAA
Done.