Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018042.1 Corchorus olitorius cultivar O-4 contig18075, 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: 76900
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:756 original size:11 final size:10
Alignment explanation
Indices: 736--823 Score: 59
Period size: 10 Copynumber: 8.0 Consensus size: 10
726 CCCAAGCCTG
* *
736 GAAAAGAAAG
1 GAAAAAAAAA
746 GAAAAAAAAA
1 GAAAAAAAAA
* *
756 GAAGAGAAAA
1 GAAAAAAAAA
766 GAAAAAGGAAAA
1 GAAAAA--AAAA
778 GGAAAAGGAAAAAA
1 -G-AAA--AAAAAA
*
792 GAAAAATAAA
1 GAAAAAAAAA
802 GAAAAATAAAA
1 GAAAAA-AAAA
813 GAAAAATAAAA
1 GAAAAA-AAAA
824 ATAAAGAAGA
Statistics
Matches: 63, Mismatches: 8, Indels: 13
0.75 0.10 0.15
Matches are distributed among these distances:
10 31 0.49
11 14 0.22
12 7 0.11
13 2 0.03
14 7 0.11
16 2 0.03
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.03
Consensus pattern (10 bp):
GAAAAAAAAA
Found at i:763 original size:5 final size:5
Alignment explanation
Indices: 736--817 Score: 53
Period size: 5 Copynumber: 16.0 Consensus size: 5
726 CCCAAGCCTG
* * *
736 GAAAA GAAAG GAAAA AAAAA GAAGA GAAAA GAAAAA GGAAAA GGAAAA
1 GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA G-AAAA -GAAAA -GAAAA
* *
784 G-GAA -AAAA GAAAA -ATAAA GAAAAA TAAAA GAAAA
1 GAAAA GAAAA GAAAA GA-AAA G-AAAA GAAAA GAAAA
818 ATAAAAATAA
Statistics
Matches: 60, Mismatches: 10, Indels: 14
0.71 0.12 0.17
Matches are distributed among these distances:
4 5 0.08
5 36 0.60
6 17 0.28
7 2 0.03
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (5 bp):
GAAAA
Found at i:3759 original size:15 final size:16
Alignment explanation
Indices: 3734--3775 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
3724 TGTTGTTTCA
*
3734 ACCTTTGCCGTAT-CC
1 ACCTATGCCGTATGCC
*
3749 ACGTATGCCGT-TGCC
1 ACCTATGCCGTATGCC
3764 ACCTATGCCGTA
1 ACCTATGCCGTA
3776 CCAACCCTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
14 1 0.05
15 21 0.95
ACGTcount: A:0.17, C:0.36, G:0.19, T:0.29
Consensus pattern (16 bp):
ACCTATGCCGTATGCC
Found at i:7112 original size:13 final size:13
Alignment explanation
Indices: 7096--7121 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
7086 GGCTGGCCTG
7096 GCGCGGCCCAGGC
1 GCGCGGCCCAGGC
7109 GCGCGGCCCAGGC
1 GCGCGGCCCAGGC
7122 CAGGCTTGGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.46, G:0.46, T:0.00
Consensus pattern (13 bp):
GCGCGGCCCAGGC
Found at i:7160 original size:12 final size:12
Alignment explanation
Indices: 7140--7205 Score: 51
Period size: 12 Copynumber: 5.2 Consensus size: 12
7130 GGCCTAGTGG
*
7140 AAAAGAAAGGAA
1 AAAAAAAAGGAA
7152 AAAAAAAAGAAGAGA
1 AAAAAAAAG--GA-A
7167 AAAGAAAAAGGAA
1 AAA-AAAAAGGAA
**
7180 AAGGAAAAGGAA
1 AAAAAAAAGGAA
**
7192 AAGGAAAAGGAA
1 AAAAAAAAGGAA
7204 AA
1 AA
7206 GGAAAAAAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
12 30 0.64
13 3 0.06
14 4 0.09
15 4 0.09
16 6 0.13
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (12 bp):
AAAAAAAAGGAA
Found at i:7186 original size:18 final size:18
Alignment explanation
Indices: 7145--7212 Score: 86
Period size: 18 Copynumber: 3.8 Consensus size: 18
7135 AGTGGAAAAG
*
7145 AAAGGAAAA-AAAAAAGA
1 AAAGGAAAAGAAAAAGGA
*
7162 AGA-GAAAAGAAAAAGGA
1 AAAGGAAAAGAAAAAGGA
*
7179 AAAGGAAAAGGAAAAGGA
1 AAAGGAAAAGAAAAAGGA
7197 AAAGGAAAAGGAAAAA
1 AAAGGAAAA-GAAAAA
7213 AAATAAAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
16 5 0.12
17 11 0.26
18 22 0.51
19 5 0.12
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (18 bp):
AAAGGAAAAGAAAAAGGA
Found at i:7206 original size:12 final size:12
Alignment explanation
Indices: 7165--7211 Score: 85
Period size: 12 Copynumber: 3.9 Consensus size: 12
7155 AAAAAGAAGA
*
7165 GAAAAGAAAAAG
1 GAAAAGGAAAAG
7177 GAAAAGGAAAAG
1 GAAAAGGAAAAG
7189 GAAAAGGAAAAG
1 GAAAAGGAAAAG
7201 GAAAAGGAAAA
1 GAAAAGGAAAA
7212 AAAATAAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 34 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (12 bp):
GAAAAGGAAAAG
Found at i:27971 original size:19 final size:18
Alignment explanation
Indices: 27947--27989 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
27937 ATAATCACAA
*
27947 TTCTAGATCTATTTTTCTC
1 TTCTAGATCTAGTTTT-TC
* *
27966 TTCTAGTTTTAGTTTTTC
1 TTCTAGATCTAGTTTTTC
27984 TTCTAG
1 TTCTAG
27990 TTTTTAGGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.14, C:0.16, G:0.09, T:0.60
Consensus pattern (18 bp):
TTCTAGATCTAGTTTTTC
Found at i:30802 original size:44 final size:45
Alignment explanation
Indices: 30643--30812 Score: 270
Period size: 45 Copynumber: 3.8 Consensus size: 45
30633 AAAAGAATGT
30643 TTTCTATTTAAGTAATTCCAAAAGAAGATTTTGGAAAATAAAAGC
1 TTTCTATTTAAGTAATTCCAAAAGAAGATTTTGGAAAATAAAAGC
* *
30688 TTTCTATTTAAATAATTCCAAAAGAAGATTTCGGAAAATAAAAGC
1 TTTCTATTTAAGTAATTCCAAAAGAAGATTTTGGAAAATAAAAGC
* * *
30733 TTTCTATTTAAGTAATTCCAAAAGAAGATTTTGGAAAACAAAGGT
1 TTTCTATTTAAGTAATTCCAAAAGAAGATTTTGGAAAATAAAAGC
* *
30778 TTTCT-TTTAAGTAGTTCCAAAAGAAGGTTTTGGAA
1 TTTCTATTTAAGTAATTCCAAAAGAAGATTTTGGAA
30813 TTCAATAAAA
Statistics
Matches: 116, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
44 28 0.24
45 88 0.76
ACGTcount: A:0.42, C:0.09, G:0.15, T:0.34
Consensus pattern (45 bp):
TTTCTATTTAAGTAATTCCAAAAGAAGATTTTGGAAAATAAAAGC
Found at i:32949 original size:22 final size:21
Alignment explanation
Indices: 32924--32977 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 21
32914 GAAGTTCGTG
32924 TTTGAAGACTTATTGAAGATAA
1 TTTGAAGA-TTATTGAAGATAA
*
32946 TTTGAAGA-T-TTGAAGATCA
1 TTTGAAGATTATTGAAGATAA
32965 -TTGAAGAATTATT
1 TTTGAAG-ATTATT
32978 TCAAGAAGCA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 6 0.21
19 10 0.36
20 2 0.07
21 2 0.07
22 8 0.29
ACGTcount: A:0.39, C:0.04, G:0.19, T:0.39
Consensus pattern (21 bp):
TTTGAAGATTATTGAAGATAA
Found at i:36202 original size:21 final size:20
Alignment explanation
Indices: 36164--36202 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
36154 GGGATTGTTC
* *
36164 CTAAATAAAAATTGTTTTTG
1 CTAAAGAAAAAGTGTTTTTG
36184 CTAAAGAAAAAGTGTTTTT
1 CTAAAGAAAAAGTGTTTTT
36203 CTCAAAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.41, C:0.05, G:0.13, T:0.41
Consensus pattern (20 bp):
CTAAAGAAAAAGTGTTTTTG
Found at i:38217 original size:65 final size:65
Alignment explanation
Indices: 37966--38219 Score: 298
Period size: 65 Copynumber: 3.9 Consensus size: 65
37956 GAAAACTTTT
* * * * * *
37966 AGAAGTACACCGGAAGACGGTTTCTTAGAAAAAGTTTTTAAAAGTTG-TCGGAAGATGATCTTGT
1 AGAAGTACACCAGAAGATGGTTTC-T-CAAAGAGTTTTCAAAAGTTGATCGGAAGACGATCTTGT
38030 TA
64 TA
* * * * *
38032 AGAACTAGACCAGAAGATGGTCTCTCAAAGAGTTTTCAAAAGTTGATCGGACGATGATCTTGTTA
1 AGAAGTACACCAGAAGATGGTTTCTCAAAGAGTTTTCAAAAGTTGATCGGAAGACGATCTTGTTA
** *
38097 AGAAGTACACCAGAAGCGGGTTTCTCAAAGAGTTTTCAGAAA-TGGATCAGG-AGACGATCTTGT
1 AGAAGTACACCAGAAGATGGTTTCTCAAAGAGTTTTCA-AAAGTTGATC-GGAAGACGATCTTGT
*
38160 CA
64 TA
* *
38162 AGAAGTACACTAGAAGATGGTTTCTCAAAGAGTTTTCAGAAGTTGATCGGAAGACGAT
1 AGAAGTACACCAGAAGATGGTTTCTCAAAGAGTTTTCAAAAGTTGATCGGAAGACGAT
38220 GTTCTTCATA
Statistics
Matches: 160, Mismatches: 23, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
64 21 0.13
65 115 0.72
66 24 0.15
ACGTcount: A:0.35, C:0.14, G:0.25, T:0.27
Consensus pattern (65 bp):
AGAAGTACACCAGAAGATGGTTTCTCAAAGAGTTTTCAAAAGTTGATCGGAAGACGATCTTGTTA
Found at i:39044 original size:21 final size:22
Alignment explanation
Indices: 39018--39059 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 22
39008 CAAGAACCAA
39018 AATCAACCATCAAAAC-AAATT
1 AATCAACCATCAAAACGAAATT
39039 AATCAACCATCAAAACGAAAT
1 AATCAACCATCAAAACGAAAT
39060 CATCATCACC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.57, C:0.24, G:0.02, T:0.17
Consensus pattern (22 bp):
AATCAACCATCAAAACGAAATT
Found at i:41829 original size:29 final size:29
Alignment explanation
Indices: 41792--41848 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
41782 ACCTTTGTTT
*
41792 TTGTATTTGTTCAAGTGCGGGTTGTGCAG
1 TTGTATTTGTTCAACTGCGGGTTGTGCAG
* *
41821 TTGTGTTTGTTCAACTGTGGGTTGTGCA
1 TTGTATTTGTTCAACTGCGGGTTGTGCA
41849 CTTGGGATTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.12, C:0.11, G:0.33, T:0.44
Consensus pattern (29 bp):
TTGTATTTGTTCAACTGCGGGTTGTGCAG
Found at i:41859 original size:29 final size:29
Alignment explanation
Indices: 41798--41860 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 29
41788 GTTTTTGTAT
* * * *
41798 TTGTTCAAGTGCGGGTTGTGCAGTTGTGT
1 TTGTTCAACTGCGGGTTGTGCACTTGGGA
*
41827 TTGTTCAACTGTGGGTTGTGCACTTGGGA
1 TTGTTCAACTGCGGGTTGTGCACTTGGGA
41856 TTGTT
1 TTGTT
41861 TTGAGTGTGG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.11, C:0.11, G:0.35, T:0.43
Consensus pattern (29 bp):
TTGTTCAACTGCGGGTTGTGCACTTGGGA
Found at i:56224 original size:42 final size:42
Alignment explanation
Indices: 56145--56224 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
56135 CGCGCCATTC
* * * *
56145 CAAGCCTCATCCGAGCCTCATGCCCGGCCATGCCCGGCACCA
1 CAAGCCCCATCCGAACCTCATGCCCGGCCAGGACCGGCACCA
* *
56187 CAAGCCCCGTCCGAACCTCATGCCCGGCTAGGACCGGC
1 CAAGCCCCATCCGAACCTCATGCCCGGCCAGGACCGGC
56225 CACAGTCAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.19, C:0.46, G:0.24, T:0.11
Consensus pattern (42 bp):
CAAGCCCCATCCGAACCTCATGCCCGGCCAGGACCGGCACCA
Found at i:59611 original size:52 final size:52
Alignment explanation
Indices: 59554--59708 Score: 240
Period size: 52 Copynumber: 3.0 Consensus size: 52
59544 ATTTCACTCA
* * *
59554 AGTCTTTAAAGTATTCAATTTAGCTCCTTTTCAAGTCGGGAAAGTTCTCACC
1 AGTCTTCAAAGTATTCAATTTAGCTCTTTTTCAAGTCGGGAAAGTTCCCACC
*
59606 AGTCTTCAAAGTATTCAATTTAGTTCTTTTTCAAGTCGGGAAAGTTCCCACC
1 AGTCTTCAAAGTATTCAATTTAGCTCTTTTTCAAGTCGGGAAAGTTCCCACC
* *
59658 AGTCTTCAAAGTATTCAATTTAGCTCTTTTTC-CGATTGGGAAAGTTCCCAC
1 AGTCTTCAAAGTATTCAATTTAGCTCTTTTTCAAG-TCGGGAAAGTTCCCAC
59709 TAAGTTTTTA
Statistics
Matches: 95, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
51 1 0.01
52 94 0.99
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.37
Consensus pattern (52 bp):
AGTCTTCAAAGTATTCAATTTAGCTCTTTTTCAAGTCGGGAAAGTTCCCACC
Found at i:59725 original size:36 final size:38
Alignment explanation
Indices: 59685--59788 Score: 121
Period size: 36 Copynumber: 2.9 Consensus size: 38
59675 ATTTAGCTCT
59685 TTTTCCGATTGGGAAAGTTCCCACT-AAG-TTTTTAAG
1 TTTTCCGATTGGGAAAGTTCCCACTCAAGTTTTTTAAG
*
59721 TTTT-CGAATTGGGAAGGTTCCCA-TCAAGTTTTTTAAG
1 TTTTCCG-ATTGGGAAAGTTCCCACTCAAGTTTTTTAAG
* **
59758 CTTTCAAATTGGGAAAGTTCCCAC-C-AGTTTT
1 TTTTCCGATTGGGAAAGTTCCCACTCAAGTTTT
59789 CAACGTATTC
Statistics
Matches: 58, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
35 3 0.05
36 28 0.48
37 27 0.47
ACGTcount: A:0.25, C:0.17, G:0.19, T:0.38
Consensus pattern (38 bp):
TTTTCCGATTGGGAAAGTTCCCACTCAAGTTTTTTAAG
Found at i:59768 original size:37 final size:36
Alignment explanation
Indices: 59692--59788 Score: 133
Period size: 37 Copynumber: 2.7 Consensus size: 36
59682 TCTTTTTCCG
* *
59692 ATTGGGAAAGTTCCCACTAAG-TTTTTAAGTTTTCGA
1 ATTGGGAAAGTTCCCAC-AAGTTTTTTAAGCTTTCAA
*
59728 ATTGGGAAGGTTCCCATCAAGTTTTTTAAGCTTTCAA
1 ATTGGGAAAGTTCCCA-CAAGTTTTTTAAGCTTTCAA
*
59765 ATTGGGAAAGTTCCCACCAGTTTT
1 ATTGGGAAAGTTCCCACAAGTTTT
59789 CAACGTATTC
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
36 25 0.46
37 29 0.54
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (36 bp):
ATTGGGAAAGTTCCCACAAGTTTTTTAAGCTTTCAA
Found at i:61379 original size:52 final size:52
Alignment explanation
Indices: 61316--61470 Score: 247
Period size: 52 Copynumber: 3.0 Consensus size: 52
61306 ATTTAACTCA
* * * **
61316 AGTCTTTAAAGTATTCAATTTAGCTCCTTTTCAAGTCGGGAATGTTTTCACC
1 AGTCTTCAAAGTATTCAATTTAGCTCTTTTTCAAGTCGGGAAAGTTCCCACC
61368 AGTCTTCAAAGTATTCAATTTAGCTCTTTTTCAAGTCGGGAAAGTTCCCACC
1 AGTCTTCAAAGTATTCAATTTAGCTCTTTTTCAAGTCGGGAAAGTTCCCACC
* *
61420 AGTCTTCAAAGTATTCAATTTAGCTCTTTTTCAAATTGGGAAAGTTCCCAC
1 AGTCTTCAAAGTATTCAATTTAGCTCTTTTTCAAGTCGGGAAAGTTCCCAC
61471 TAAGTTTTTA
Statistics
Matches: 96, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 96 1.00
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.37
Consensus pattern (52 bp):
AGTCTTCAAAGTATTCAATTTAGCTCTTTTTCAAGTCGGGAAAGTTCCCACC
Found at i:61561 original size:36 final size:35
Alignment explanation
Indices: 61447--61549 Score: 161
Period size: 36 Copynumber: 2.9 Consensus size: 35
61437 ATTTAGCTCT
61447 TTTTCAAATTGGGAAAGTTCCCACTAAGTTTTTAAG
1 TTTTCAAATTGGGAAAGTTCCCAC-AAGTTTTTAAG
*
61483 TTTTCAAATTGGGAAGGTTCCCATCAAGTTTTTAAG
1 TTTTCAAATTGGGAAAGTTCCCA-CAAGTTTTTAAG
* *
61519 TTTTCAAATTGGGAAACTTCCCACCAGTTTT
1 TTTTCAAATTGGGAAAGTTCCCACAAGTTTT
61550 CAAAGTATTC
Statistics
Matches: 62, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
35 7 0.11
36 54 0.87
37 1 0.02
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.39
Consensus pattern (35 bp):
TTTTCAAATTGGGAAAGTTCCCACAAGTTTTTAAG
Found at i:62990 original size:14 final size:14
Alignment explanation
Indices: 62971--63000 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
62961 TCTATTAGTT
*
62971 TTCAAAAATAAAAA
1 TTCAAAAAGAAAAA
62985 TTCAAAAAGAAAAA
1 TTCAAAAAGAAAAA
62999 TT
1 TT
63001 GAGTATTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.67, C:0.07, G:0.03, T:0.23
Consensus pattern (14 bp):
TTCAAAAAGAAAAA
Found at i:63229 original size:52 final size:52
Alignment explanation
Indices: 63078--63232 Score: 238
Period size: 52 Copynumber: 3.0 Consensus size: 52
63068 ATTTCACTCA
* * *
63078 AGTCTTTAAAGTATTCGATTTAGCTCTTTTTCAAGTCGGGAAAGTTCTCACC
1 AGTCTTCAAAGTATTCAATTTAGCTCTTTTTCAAGTCGGGAAAGTTCCCACC
* * *
63130 AATCTTCAAAGTATTCAATTTAGCTCTTTCTCAAGTCCGGAAAGTTCCCACC
1 AGTCTTCAAAGTATTCAATTTAGCTCTTTTTCAAGTCGGGAAAGTTCCCACC
* *
63182 AGTCTTCAAAGTATTCAATTTAGCTCTTTTTCAAATTGGGAAAGTTCCCAC
1 AGTCTTCAAAGTATTCAATTTAGCTCTTTTTCAAGTCGGGAAAGTTCCCAC
63233 TAAGTTTTTA
Statistics
Matches: 92, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
52 92 1.00
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.36
Consensus pattern (52 bp):
AGTCTTCAAAGTATTCAATTTAGCTCTTTTTCAAGTCGGGAAAGTTCCCACC
Found at i:63249 original size:36 final size:37
Alignment explanation
Indices: 63209--63311 Score: 151
Period size: 36 Copynumber: 2.9 Consensus size: 37
63199 ATTTAGCTCT
63209 TTTTCAAATTGGGAAAGTTCCCACT-AAGTTTTTAAA
1 TTTTCAAATTGGGAAAGTTCCCACTCAAGTTTTTAAA
* *
63245 TTTTCAAATTGGGAAGGTTCCCA-TCAAGTTTTTAAG
1 TTTTCAAATTGGGAAAGTTCCCACTCAAGTTTTTAAA
*
63281 TTTTCAAATTGGGAAACTTCCCAC-C-AGTTTT
1 TTTTCAAATTGGGAAAGTTCCCACTCAAGTTTT
63312 CAAAGTATTC
Statistics
Matches: 61, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
35 7 0.11
36 54 0.89
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.39
Consensus pattern (37 bp):
TTTTCAAATTGGGAAAGTTCCCACTCAAGTTTTTAAA
Found at i:63323 original size:36 final size:35
Alignment explanation
Indices: 63209--63323 Score: 142
Period size: 36 Copynumber: 3.2 Consensus size: 35
63199 ATTTAGCTCT
63209 TTTTCAAATTGGGAAAGTTCCCACTAAGTTTTTAAA-
1 TTTTCAAATTGGGAAAGTTCCCAC-AAG-TTTTAAAG
* *
63245 TTTTCAAATTGGGAAGGTTCCCATCAAGTTTTTAAG
1 TTTTCAAATTGGGAAAGTTCCCA-CAAGTTTTAAAG
* *
63281 TTTTCAAATTGGGAAACTTCCCACCAGTTTTCAAAG
1 TTTTCAAATTGGGAAAGTTCCCACAAGTTTT-AAAG
*
63317 TATTCAA
1 TTTTCAA
63324 TCTAGCTCTT
Statistics
Matches: 69, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
35 13 0.19
36 55 0.80
37 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (35 bp):
TTTTCAAATTGGGAAAGTTCCCACAAGTTTTAAAG
Found at i:70199 original size:76 final size:76
Alignment explanation
Indices: 70062--70213 Score: 191
Period size: 76 Copynumber: 2.0 Consensus size: 76
70052 ACAAGGACCC
* * * *
70062 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAACACCCATGTGGTTTGCTTGAGGACCCAGGT
1 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAACACACATGTGGTTTGCCTGAGCACCCAGAT
70127 GGGCTGTGTCA
66 GGGCTGTGTCA
* * * * *
70138 CGACTCCAGCTGGGTGCCCACATGGTTTGTC-TGAAGACACATGT-GTTTCGCCTGATCACCCAG
1 CGACTCCACCTGGGCGCCCACATGG-TTGCCTTGAACACACATGTGGTTT-GCCTGAGCACCCAG
70201 ATGGGCTGTGTCA
64 ATGGGCTGTGTCA
70214 TAGCTCATCA
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
75 4 0.06
76 57 0.88
77 4 0.06
ACGTcount: A:0.17, C:0.29, G:0.29, T:0.25
Consensus pattern (76 bp):
CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAACACACATGTGGTTTGCCTGAGCACCCAGAT
GGGCTGTGTCA
Found at i:71256 original size:3 final size:3
Alignment explanation
Indices: 71248--71305 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
71238 GTTACTAACC
71248 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
71296 TTA TTA TTA T
1 TTA TTA TTA T
71306 GATATATTTT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:76238 original size:20 final size:20
Alignment explanation
Indices: 76213--76252 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
76203 CAACCAATTT
76213 AAAAAAAAAAAAAGAAAAGA
1 AAAAAAAAAAAAAGAAAAGA
* * *
76233 AAAAAAGAAAGAAGAGAAGA
1 AAAAAAAAAAAAAGAAAAGA
76253 GAAGAGAATG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.00
Consensus pattern (20 bp):
AAAAAAAAAAAAAGAAAAGA
Found at i:76257 original size:17 final size:17
Alignment explanation
Indices: 76215--76250 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
76205 ACCAATTTAA
*
76215 AAAAAAAAAAAGAAAAG
1 AAAAAAAGAAAGAAAAG
*
76232 AAAAAAAGAAAGAAGAG
1 AAAAAAAGAAAGAAAAG
76249 AA
1 AA
76251 GAGAAGAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (17 bp):
AAAAAAAGAAAGAAAAG
Done.