Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009605.1 Corchorus capsularis cultivar CVL-1 contig09626, 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: 77778
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:5756 original size:7 final size:7
Alignment explanation
Indices: 5744--5774 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
5734 GAAAAGGAGA
5744 GAATGAG
1 GAATGAG
5751 GAATGA-
1 GAATGAG
5757 GAATGAG
1 GAATGAG
5764 GAATGAG
1 GAATGAG
5771 GAAT
1 GAAT
5775 TAATTGGAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.45, C:0.00, G:0.39, T:0.16
Consensus pattern (7 bp):
GAATGAG
Found at i:5760 original size:13 final size:13
Alignment explanation
Indices: 5742--5770 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
5732 AAGAAAAGGA
5742 GAGAATGAGGAAT
1 GAGAATGAGGAAT
5755 GAGAATGAGGAAT
1 GAGAATGAGGAAT
5768 GAG
1 GAG
5771 GAATTAATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.41, T:0.14
Consensus pattern (13 bp):
GAGAATGAGGAAT
Found at i:14778 original size:45 final size:45
Alignment explanation
Indices: 14714--14806 Score: 150
Period size: 45 Copynumber: 2.1 Consensus size: 45
14704 CCAGTCTGAT
* *
14714 TTTCTCCACTCAACAAACTTTGGATTTTCTTTAGGAGGACTTCTG
1 TTTCTCCACTCAACAAACTTTGGATTTTCCTTAGGAGGACTTCCG
* *
14759 TTTCTCCACTCAGCAAACTTTGGATTTTCCTTAGGAGGAGTTCCG
1 TTTCTCCACTCAACAAACTTTGGATTTTCCTTAGGAGGACTTCCG
14804 TTT
1 TTT
14807 GTGGTATCAC
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.20, C:0.23, G:0.17, T:0.40
Consensus pattern (45 bp):
TTTCTCCACTCAACAAACTTTGGATTTTCCTTAGGAGGACTTCCG
Found at i:16026 original size:282 final size:282
Alignment explanation
Indices: 15522--16364 Score: 1544
Period size: 282 Copynumber: 3.0 Consensus size: 282
15512 AGTGATCACT
* * *
15522 CATACTCTCTTCCACTTGTTTTGCTCCTCTTTGTCCCAACAGGTT-TCCATAACATATCACATAT
1 CATACTCTCTTCCACTTGTTTTGCTCCTCTCTGTCCCAATAGGTTCTCCATGACATATCACATAT
* *
15586 ATTAAAATAACAAACAATCAAATCTTCAAATAAGCTCATTTTTTTACTTCACTTGGTTTGTTGTT
66 ATTAAAATAACAAACAATCAAATCTTCAAATAAGCTCA-TTTCTAACTTCACTTGGTTTGTTGTT
* * *
15651 AAGCTCATTTCTGTCACTCCCTTTATCTGGAAATGTAATTCCAAATCCAATCAACAGAAAAATGG
130 AAGCTCATTTCTTTCACTCCCTTTATCTGGAAATGTAATGCCAAATCCAATCAACACAAAAATGG
* *
15716 AAGTTCATTTCAAGTTTTCTTAAATATAATTGATGCAAAACATGAATGAGAATTGGGAAGCTATA
195 AAGTTCAATTCAAGTTTTCTTAAATATAATTGATGCAAAACATGAATGAGAATTGAGAAGCTATA
15781 TAAACATATTGTTCTCCCATACA
260 TAAACATATTGTTCTCCCATACA
15804 CATACTCTCTTCCACTTGTTTTGCTCCTCTCTGTCCCAATAGGTTCTCCATGACATATCACATAT
1 CATACTCTCTTCCACTTGTTTTGCTCCTCTCTGTCCCAATAGGTTCTCCATGACATATCACATAT
*
15869 ATTAAAATAACAAACAATCAAATCTTCAAATAAGCTCATTTCTGACTTCACTTGGTTTGTTGTTA
66 ATTAAAATAACAAACAATCAAATCTTCAAATAAGCTCATTTCTAACTTCACTTGGTTTGTTGTTA
15934 AGCTCATTTCTTTCACTCCCTTTATCTGGAAATGTAATGCCAAATCCAATCAACACAAAAATGGA
131 AGCTCATTTCTTTCACTCCCTTTATCTGGAAATGTAATGCCAAATCCAATCAACACAAAAATGGA
*
15999 AGTTCAATTCAAGTTTTCTTAAATATAATTGATGCAAAACATGAATGAGAATTGAGAAACTATAT
196 AGTTCAATTCAAGTTTTCTTAAATATAATTGATGCAAAACATGAATGAGAATTGAGAAGCTATAT
16064 AAACATATTGTTCTCCCATACA
261 AAACATATTGTTCTCCCATACA
16086 CATACTCTCTTCCACTTGTTTTGCTCCTCTCTGTCCCAATAGGTTCTCCATGACATATCACATAT
1 CATACTCTCTTCCACTTGTTTTGCTCCTCTCTGTCCCAATAGGTTCTCCATGACATATCACATAT
16151 ATTAAAATAACAAACAATCAAATCTTCAAATAAGCTCATTTCTAACTTCACTTGGTTTGTTGTTA
66 ATTAAAATAACAAACAATCAAATCTTCAAATAAGCTCATTTCTAACTTCACTTGGTTTGTTGTTA
16216 AGCTCATTTCTTTCACTCCCTTTATCTGGAAATGTAATGCCAAATCCAATCAACACAAAAATGGA
131 AGCTCATTTCTTTCACTCCCTTTATCTGGAAATGTAATGCCAAATCCAATCAACACAAAAATGGA
16281 AGTTCAATTCAAGTTTTCTTAAATATAATTGATGCAAAACATGAATGAGAATTGAGAAGCTATAT
196 AGTTCAATTCAAGTTTTCTTAAATATAATTGATGCAAAACATGAATGAGAATTGAGAAGCTATAT
**
16346 AAACATACCGTTCTCCCAT
261 AAACATATTGTTCTCCCAT
16365 TGAACATCTT
Statistics
Matches: 545, Mismatches: 15, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
282 489 0.90
283 56 0.10
ACGTcount: A:0.34, C:0.21, G:0.10, T:0.35
Consensus pattern (282 bp):
CATACTCTCTTCCACTTGTTTTGCTCCTCTCTGTCCCAATAGGTTCTCCATGACATATCACATAT
ATTAAAATAACAAACAATCAAATCTTCAAATAAGCTCATTTCTAACTTCACTTGGTTTGTTGTTA
AGCTCATTTCTTTCACTCCCTTTATCTGGAAATGTAATGCCAAATCCAATCAACACAAAAATGGA
AGTTCAATTCAAGTTTTCTTAAATATAATTGATGCAAAACATGAATGAGAATTGAGAAGCTATAT
AAACATATTGTTCTCCCATACA
Found at i:18736 original size:78 final size:78
Alignment explanation
Indices: 18649--18895 Score: 388
Period size: 78 Copynumber: 3.2 Consensus size: 78
18639 ATTTTTTAAT
** * *
18649 TAAAATAGTAAAATATTAAAATATAATAGTTATAAGGTTAATAGATTTAATTATATAAAAATAGA
1 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
*
18714 GTTTTTAGTTGAA
66 GTTTTTAGTTGAG
*
18727 TAAAATAGTAAAATGGTAAAGTATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
1 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
18792 GTTTTTAGTTGAG
66 GTTTTTAGTTGAG
* * * *
18805 TAAAATAGTAAAATGGTAAAATAAAATAGTTATAAAGATATTATATTTAATTAAATAAAAATAGA
1 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
18870 GTTTTTAGTTGAG
66 GTTTTTAGTTGAG
18883 TAAAACTA-TAAAA
1 TAAAA-TAGTAAAA
18896 ACCTAAACAA
Statistics
Matches: 157, Mismatches: 11, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
78 155 0.99
79 2 0.01
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.36
Consensus pattern (78 bp):
TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
GTTTTTAGTTGAG
Found at i:24607 original size:52 final size:52
Alignment explanation
Indices: 24551--24655 Score: 210
Period size: 52 Copynumber: 2.0 Consensus size: 52
24541 AACTCCCTTA
24551 GTTTTTCATATCAAAAATCGAATTTAATCGCCTTTCCCCTGTCTGATCTGCT
1 GTTTTTCATATCAAAAATCGAATTTAATCGCCTTTCCCCTGTCTGATCTGCT
24603 GTTTTTCATATCAAAAATCGAATTTAATCGCCTTTCCCCTGTCTGATCTGCT
1 GTTTTTCATATCAAAAATCGAATTTAATCGCCTTTCCCCTGTCTGATCTGCT
24655 G
1 G
24656 CAGTTGTGCT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.23, C:0.25, G:0.12, T:0.40
Consensus pattern (52 bp):
GTTTTTCATATCAAAAATCGAATTTAATCGCCTTTCCCCTGTCTGATCTGCT
Found at i:24831 original size:22 final size:22
Alignment explanation
Indices: 24793--24852 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 22
24783 AAAACCTCTA
* *
24793 TATG-AATTGTCAGTAATCGCAC
1 TATGAAATTGTGA-TAATCACAC
* * *
24815 TCTGAAATTTTGATAATCATAC
1 TATGAAATTGTGATAATCACAC
24837 TATGAAATTGTGATAA
1 TATGAAATTGTGATAA
24853 CCTCGTTATG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
22 24 0.80
23 6 0.20
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.37
Consensus pattern (22 bp):
TATGAAATTGTGATAATCACAC
Found at i:24900 original size:45 final size:44
Alignment explanation
Indices: 24817--24901 Score: 116
Period size: 45 Copynumber: 1.9 Consensus size: 44
24807 AATCGCACTC
* *
24817 TGAAATTTTGATAATCATACTATGAAATTGTGATAACCTCGTTA
1 TGAAATTTTGATAATCATACAATAAAATTGTGATAACCTCGTTA
* * *
24861 TGAAATTTTGATAAATCTTCCAATAAAATTTTGATAACCTC
1 TGAAATTTTGAT-AATCATACAATAAAATTGTGATAACCTC
24902 ATGAAATCTT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
44 12 0.34
45 23 0.66
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.39
Consensus pattern (44 bp):
TGAAATTTTGATAATCATACAATAAAATTGTGATAACCTCGTTA
Found at i:24950 original size:22 final size:22
Alignment explanation
Indices: 24921--25038 Score: 132
Period size: 22 Copynumber: 5.5 Consensus size: 22
24911 TGATGACTAC
24921 AAATTTTGATAACCTCCCTATG
1 AAATTTTGATAACCTCCCTATG
** ** *
24943 ATTTTTTGATAACCTCATTATA
1 AAATTTTGATAACCTCCCTATG
* *
24965 AAATTTTGTTAATCTCCCTATG
1 AAATTTTGATAACCTCCCTATG
* *
24987 AAATTTTGATAACCTTCATATG
1 AAATTTTGATAACCTCCCTATG
*
25009 AAATTTTGATATCCT-CC-ATG
1 AAATTTTGATAACCTCCCTATG
25029 AAATTTTGAT
1 AAATTTTGAT
25039 TACTCCTAAT
Statistics
Matches: 78, Mismatches: 18, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
20 13 0.17
21 1 0.01
22 64 0.82
ACGTcount: A:0.32, C:0.16, G:0.08, T:0.43
Consensus pattern (22 bp):
AAATTTTGATAACCTCCCTATG
Found at i:24984 original size:44 final size:44
Alignment explanation
Indices: 24921--25038 Score: 152
Period size: 44 Copynumber: 2.7 Consensus size: 44
24911 TGATGACTAC
**
24921 AAATTTTGATAACCTCCCTATGATTTTTTGATAACC-TCATTATA
1 AAATTTTGATAACCTCCCTATGAAATTTTGATAACCTTCA-TATA
* * *
24965 AAATTTTGTTAATCTCCCTATGAAATTTTGATAACCTTCATATG
1 AAATTTTGATAACCTCCCTATGAAATTTTGATAACCTTCATATA
*
25009 AAATTTTGATATCCT-CC-ATGAAATTTTGAT
1 AAATTTTGATAACCTCCCTATGAAATTTTGAT
25039 TACTCCTAAT
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
42 13 0.20
43 2 0.03
44 47 0.72
45 3 0.05
ACGTcount: A:0.32, C:0.16, G:0.08, T:0.43
Consensus pattern (44 bp):
AAATTTTGATAACCTCCCTATGAAATTTTGATAACCTTCATATA
Found at i:25031 original size:20 final size:22
Alignment explanation
Indices: 24817--25038 Score: 91
Period size: 22 Copynumber: 10.5 Consensus size: 22
24807 AATCGCACTC
* *
24817 TGAAATTTTGATAATCAT-ACTA
1 TGAAATTTTGATAACCTTCAC-A
* **
24839 TGAAATTGTGATAACC-TCGTTA
1 TGAAATTTTGATAACCTTC-ACA
*
24861 TGAAATTTTGATAAATCTTC-CAA
1 TGAAATTTTGAT-AACCTTCAC-A
*
24884 TAAAATTTTGATAACC-T--CA
1 TGAAATTTTGATAACCTTCACA
* *
24903 TGAAATCTTGATGA-C-T-AC-
1 TGAAATTTTGATAACCTTCACA
*
24921 --AAATTTTGATAACC-TCCCTA
1 TGAAATTTTGATAACCTTCAC-A
** *
24941 TGATTTTTTGATAACC-TCATTA
1 TGAAATTTTGATAACCTTCA-CA
* * * *
24963 TAAAATTTTGTTAATC-TCCCTA
1 TGAAATTTTGATAACCTTCAC-A
*
24985 TGAAATTTTGATAACCTTCATA
1 TGAAATTTTGATAACCTTCACA
*
25007 TGAAATTTTGATATCC-TC-CA
1 TGAAATTTTGATAACCTTCACA
25027 TGAAATTTTGAT
1 TGAAATTTTGAT
25039 TACTCCTAAT
Statistics
Matches: 152, Mismatches: 33, Indels: 32
0.70 0.15 0.15
Matches are distributed among these distances:
16 10 0.07
17 2 0.01
18 3 0.02
19 13 0.09
20 14 0.09
21 4 0.03
22 87 0.57
23 17 0.11
24 2 0.01
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.41
Consensus pattern (22 bp):
TGAAATTTTGATAACCTTCACA
Found at i:25146 original size:44 final size:44
Alignment explanation
Indices: 25095--25240 Score: 143
Period size: 44 Copynumber: 3.3 Consensus size: 44
25085 AGAAATACCA
* *
25095 CTATGAAATTTTGGTAATCATATTTTGAAAATTTGATAACCTCT
1 CTATGAAATTTTGATAATCATATTTTGAAAATTTGATAACCCCT
* * * * *
25139 TTATGAAATTTTGATAA-CCTCTCTAT-AAAATTTTGTTAACCCCT
1 CTATGAAATTTTGATAATCATAT-TTTGAAAA-TTTGATAACCCCT
* * * * *
25183 CTATGAAATTTTGATAATCACATTTTGTAATTTTGATAACCACG
1 CTATGAAATTTTGATAATCATATTTTGAAAATTTGATAACCCCT
*
25227 CTTTGAAATTTTGA
1 CTATGAAATTTTGA
25241 AATTGGATCA
Statistics
Matches: 80, Mismatches: 18, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
43 7 0.09
44 69 0.86
45 4 0.05
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (44 bp):
CTATGAAATTTTGATAATCATATTTTGAAAATTTGATAACCCCT
Found at i:25183 original size:24 final size:22
Alignment explanation
Indices: 25122--25199 Score: 104
Period size: 22 Copynumber: 3.6 Consensus size: 22
25112 TCATATTTTG
*
25122 AAAA-TTTGATAACCTCTTTAT
1 AAAATTTTGATAACCTCTCTAT
*
25143 GAAATTTTGATAACCTCTCTAT
1 AAAATTTTGATAACCTCTCTAT
* *
25165 AAAATTTTGTTAACCCCTCTAT
1 AAAATTTTGATAACCTCTCTAT
*
25187 GAAATTTTGATAA
1 AAAATTTTGATAA
25200 TCACATTTTG
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
21 3 0.06
22 46 0.94
ACGTcount: A:0.36, C:0.15, G:0.08, T:0.41
Consensus pattern (22 bp):
AAAATTTTGATAACCTCTCTAT
Found at i:25214 original size:22 final size:22
Alignment explanation
Indices: 25093--25240 Score: 100
Period size: 22 Copynumber: 6.7 Consensus size: 22
25083 CCAGAAATAC
* * *
25093 CACTATGAAATTTTGGTAATCA
1 CACTTTGAAATTTTGATAACCA
* * * *
25115 TATTTTGAAAATTTGATAACCT
1 CACTTTGAAATTTTGATAACCA
* *
25137 C-TTTATGAAATTTTGATAACCT
1 CACTT-TGAAATTTTGATAACCA
* * * * *
25159 CTCTATAAAATTTTGTTAACCC
1 CACTTTGAAATTTTGATAACCA
* * *
25181 CTCTATGAAATTTTGATAATCA
1 CACTTTGAAATTTTGATAACCA
* *
25203 CATTTTGTAATTTTGATAACCA
1 CACTTTGAAATTTTGATAACCA
*
25225 CGCTTTGAAATTTTGA
1 CACTTTGAAATTTTGA
25241 AATTGGATCA
Statistics
Matches: 98, Mismatches: 26, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
21 3 0.03
22 94 0.96
23 1 0.01
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (22 bp):
CACTTTGAAATTTTGATAACCA
Found at i:25359 original size:38 final size:37
Alignment explanation
Indices: 25317--25393 Score: 109
Period size: 38 Copynumber: 2.1 Consensus size: 37
25307 GTTGAAGACG
25317 AAGACAAAAAGCAAAATTAAATACAACGATTGGAAACA
1 AAGACAAAAAGCAAAATTAAATACAACG-TTGGAAACA
* * **
25355 AAGACCAAAGGCAAAATTAAATAGGACGTTGGAAACA
1 AAGACAAAAAGCAAAATTAAATACAACGTTGGAAACA
25392 AA
1 AA
25394 AAGTCAAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
37 11 0.31
38 24 0.69
ACGTcount: A:0.57, C:0.13, G:0.17, T:0.13
Consensus pattern (37 bp):
AAGACAAAAAGCAAAATTAAATACAACGTTGGAAACA
Found at i:25551 original size:30 final size:31
Alignment explanation
Indices: 25517--25575 Score: 102
Period size: 30 Copynumber: 1.9 Consensus size: 31
25507 TGGTAATTCA
*
25517 GAAATATGTTTTTAAAA-AAGGGTACAATTG
1 GAAATATGTTTTAAAAATAAGGGTACAATTG
25547 GAAATATGTTTTAAAAATAAGGGTACAAT
1 GAAATATGTTTTAAAAATAAGGGTACAAT
25576 CGAAAAATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 16 0.59
31 11 0.41
ACGTcount: A:0.46, C:0.03, G:0.19, T:0.32
Consensus pattern (31 bp):
GAAATATGTTTTAAAAATAAGGGTACAATTG
Found at i:25725 original size:22 final size:22
Alignment explanation
Indices: 25683--25726 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
25673 TATTTATATG
*
25683 AAATTATGATAATCTCTCTATT
1 AAATTATGATAATCTCACTATT
25705 AAATTATGATAAT-TACACTATT
1 AAATTATGATAATCT-CACTATT
25727 TTTTATGATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 1 0.05
22 19 0.95
ACGTcount: A:0.41, C:0.11, G:0.05, T:0.43
Consensus pattern (22 bp):
AAATTATGATAATCTCACTATT
Found at i:25803 original size:22 final size:22
Alignment explanation
Indices: 25741--25954 Score: 123
Period size: 22 Copynumber: 9.7 Consensus size: 22
25731 ATGATCCCAT
* * *
25741 TATGAAATTTTGTTAACCTCCC
1 TATGAAATTTTGATAACCACAC
* *
25763 TAAGAAATTTTGA-ACACCACAA
1 TATGAAATTTTGATA-ACCACAC
25785 TATGAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAACC-ACAC
* ** *
25808 TATGAGATGCT-ATAACCTC-C
1 TATGAAATTTTGATAACCACAC
* * **
25828 ATATGATATATTGATAACCACGT
1 -TATGAAATTTTGATAACCACAC
* * * * * *
25851 TATGAAAATATAAAAACCTCCC
1 TATGAAATTTTGATAACCACAC
25873 TATG-AATTGTT-AGTAACCACAC
1 TATGAAATT-TTGA-TAACCACAC
* *
25895 TCTGAAATTTTGATAATCACAC
1 TATGAAATTTTGATAACCACAC
* * *
25917 TATGAAATTATGATAACCTCGC
1 TATGAAATTTTGATAACCACAC
*
25939 TATGAAATTTTAATAA
1 TATGAAATTTTGATAA
25955 ATCTTCCTAT
Statistics
Matches: 143, Mismatches: 39, Indels: 20
0.71 0.19 0.10
Matches are distributed among these distances:
20 1 0.01
21 14 0.10
22 111 0.78
23 17 0.12
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.32
Consensus pattern (22 bp):
TATGAAATTTTGATAACCACAC
Found at i:25988 original size:25 final size:25
Alignment explanation
Indices: 25931--26004 Score: 98
Period size: 25 Copynumber: 3.0 Consensus size: 25
25921 AAATTATGAT
* *
25931 AACCTCGCTATGAAATTTT-A-ATA
1 AACCTCCCTATAAAATTTTGATATA
* *
25954 AATCTTCCTATAAAATTTTGATATA
1 AACCTCCCTATAAAATTTTGATATA
25979 AACCTCCCTATAAAATTTTGATATA
1 AACCTCCCTATAAAATTTTGATATA
26004 A
1 A
26005 TCTTTTTGGT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
23 15 0.35
24 1 0.02
25 27 0.63
ACGTcount: A:0.41, C:0.16, G:0.05, T:0.38
Consensus pattern (25 bp):
AACCTCCCTATAAAATTTTGATATA
Found at i:28504 original size:2 final size:2
Alignment explanation
Indices: 28497--28528 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
28487 CATTTACTAG
28497 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
28529 ATTCTAGTGA
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):
TA
Found at i:32852 original size:14 final size:14
Alignment explanation
Indices: 32833--32865 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
32823 TTTCTAGAAG
32833 GGGACTTATAATAT
1 GGGACTTATAATAT
32847 GGGACTTATAATAT
1 GGGACTTATAATAT
32861 GGGAC
1 GGGAC
32866 AGATGGAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.33, C:0.09, G:0.27, T:0.30
Consensus pattern (14 bp):
GGGACTTATAATAT
Found at i:34261 original size:52 final size:52
Alignment explanation
Indices: 34183--34342 Score: 320
Period size: 52 Copynumber: 3.1 Consensus size: 52
34173 TTTAGAGAGC
34183 AAACAACGATGAACAAAATCCAATGATAATTGTTGAACGTATCACAACTTTA
1 AAACAACGATGAACAAAATCCAATGATAATTGTTGAACGTATCACAACTTTA
34235 AAACAACGATGAACAAAATCCAATGATAATTGTTGAACGTATCACAACTTTA
1 AAACAACGATGAACAAAATCCAATGATAATTGTTGAACGTATCACAACTTTA
34287 AAACAACGATGAACAAAATCCAATGATAATTGTTGAACGTATCACAACTTTA
1 AAACAACGATGAACAAAATCCAATGATAATTGTTGAACGTATCACAACTTTA
34339 AAAC
1 AAAC
34343 GAGAAATCTG
Statistics
Matches: 108, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 108 1.00
ACGTcount: A:0.47, C:0.17, G:0.11, T:0.24
Consensus pattern (52 bp):
AAACAACGATGAACAAAATCCAATGATAATTGTTGAACGTATCACAACTTTA
Found at i:34684 original size:18 final size:18
Alignment explanation
Indices: 34661--34704 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
34651 TGTTTCAATT
34661 AACTAATAAACTAAACTA
1 AACTAATAAACTAAACTA
*
34679 AACTAACT-AATTAAACTA
1 AACTAA-TAAACTAAACTA
*
34697 AATTAATA
1 AACTAATA
34705 GGGTAATTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 1 0.05
18 20 0.91
19 1 0.05
ACGTcount: A:0.59, C:0.14, G:0.00, T:0.27
Consensus pattern (18 bp):
AACTAATAAACTAAACTA
Found at i:35009 original size:20 final size:20
Alignment explanation
Indices: 34984--35025 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
34974 ACTTCCCTAG
34984 TGCTTGGTTCATGCTTCATC
1 TGCTTGGTTCATGCTTCATC
35004 TGCTTGGTTCATGCTTCATC
1 TGCTTGGTTCATGCTTCATC
35024 TG
1 TG
35026 TGGATACCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (20 bp):
TGCTTGGTTCATGCTTCATC
Found at i:35624 original size:22 final size:22
Alignment explanation
Indices: 35599--35641 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
35589 AACGCTTGTA
*
35599 GGTCATGGGCATGATTTGTTCT
1 GGTCATGGGCATGACTTGTTCT
*
35621 GGTCATGTGCATGACTTGTTC
1 GGTCATGGGCATGACTTGTTC
35642 AAGTTCCTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.14, C:0.16, G:0.30, T:0.40
Consensus pattern (22 bp):
GGTCATGGGCATGACTTGTTCT
Found at i:40516 original size:23 final size:23
Alignment explanation
Indices: 40486--40529 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
40476 GATTAGTTTG
40486 TAGAGACCGAGCGAGAGTGCTCA
1 TAGAGACCGAGCGAGAGTGCTCA
40509 TAGAGACCGAGCGAGAGTGCT
1 TAGAGACCGAGCGAGAGTGCT
40530 TAAGATTGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.30, C:0.20, G:0.36, T:0.14
Consensus pattern (23 bp):
TAGAGACCGAGCGAGAGTGCTCA
Found at i:52976 original size:30 final size:29
Alignment explanation
Indices: 52881--52980 Score: 121
Period size: 30 Copynumber: 3.4 Consensus size: 29
52871 TAAATAACCA
** *
52881 TTTTGCCCCCTGAACTTGTATCGTTTAGACG
1 TTTTGCCCCCTGAACTTCAAT--TTTGGACG
* *
52912 TTTTGCCCCC-GAACTTCAATCTTGGACA
1 TTTTGCCCCCTGAACTTCAATTTTGGACG
52940 TTTTGCCCCCTGAACTTCAATTTTGGAACG
1 TTTTGCCCCCTGAACTTCAATTTTGG-ACG
52970 TTTTGCCCCCT
1 TTTTGCCCCCT
52981 CAACCTAACG
Statistics
Matches: 60, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
28 15 0.25
29 14 0.23
30 21 0.35
31 10 0.17
ACGTcount: A:0.17, C:0.30, G:0.16, T:0.37
Consensus pattern (29 bp):
TTTTGCCCCCTGAACTTCAATTTTGGACG
Found at i:53214 original size:30 final size:31
Alignment explanation
Indices: 53178--53249 Score: 98
Period size: 29 Copynumber: 2.5 Consensus size: 31
53168 CGTTAGGTTG
53178 AGGGGACAAAACGTGT-CAAAATTGAAGTTC
1 AGGGGACAAAACGTGTCCAAAATTGAAGTTC
*
53208 AGGGGACAAAA--TGTCCAAGATTGAAGTTC
1 AGGGGACAAAACGTGTCCAAAATTGAAGTTC
*
53237 -GGGGGCAAAACGT
1 AGGGGACAAAACGT
53250 CTAAACGCTA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
28 12 0.32
29 13 0.35
30 12 0.32
ACGTcount: A:0.38, C:0.14, G:0.31, T:0.18
Consensus pattern (31 bp):
AGGGGACAAAACGTGTCCAAAATTGAAGTTC
Done.