Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020979.1 Corchorus olitorius cultivar O-4 contig21012, 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: 71112
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Found at i:8916 original size:22 final size:22
Alignment explanation
Indices: 8875--8929 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
8865 ATTTTTATGA
* *
8875 AATTTTGACAACTACCCTATTAG
1 AATTTTGATAACCACCCTA-TAG
* *
8898 -ATTTTGATAACCACGCTATGG
1 AATTTTGATAACCACCCTATAG
8919 AATTTTGATAA
1 AATTTTGATAA
8930 TTTACCTATG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 2 0.07
22 25 0.93
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.36
Consensus pattern (22 bp):
AATTTTGATAACCACCCTATAG
Found at i:9871 original size:4 final size:4
Alignment explanation
Indices: 9864--9900 Score: 74
Period size: 4 Copynumber: 9.2 Consensus size: 4
9854 CACTATATAT
9864 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG A
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG A
9901 GAGAGAGGAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.24, T:0.24
Consensus pattern (4 bp):
ATAG
Found at i:12974 original size:16 final size:16
Alignment explanation
Indices: 12949--12981 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
12939 GAGAACATGA
*
12949 TTTGAGAAAAACCTTT
1 TTTGAAAAAAACCTTT
12965 TTTGAAAAAAACCTTT
1 TTTGAAAAAAACCTTT
12981 T
1 T
12982 ATTACCTCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.39
Consensus pattern (16 bp):
TTTGAAAAAAACCTTT
Found at i:13021 original size:17 final size:18
Alignment explanation
Indices: 12996--13029 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
12986 CCTCTTTTGA
12996 TTTTCTGATTTT-TTCTC
1 TTTTCTGATTTTCTTCTC
*
13013 TTTTTTGATTTTCTTCT
1 TTTTCTGATTTTCTTCT
13030 TTTCTATCTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.06, C:0.15, G:0.06, T:0.74
Consensus pattern (18 bp):
TTTTCTGATTTTCTTCTC
Found at i:14070 original size:20 final size:21
Alignment explanation
Indices: 14047--14095 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
14037 TCAAGCACTT
* *
14047 AATTGCA-AAATCAGGGGTCA
1 AATTGCATAAAGCAGGGATCA
*
14067 AATTGAATAAAGCAGGGATCA
1 AATTGCATAAAGCAGGGATCA
14088 AATTGCAT
1 AATTGCAT
14096 TAAATTAAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 6 0.25
21 18 0.75
ACGTcount: A:0.43, C:0.12, G:0.22, T:0.22
Consensus pattern (21 bp):
AATTGCATAAAGCAGGGATCA
Found at i:14980 original size:21 final size:21
Alignment explanation
Indices: 14955--14994 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
14945 CCCGAGAAGG
14955 AGGGTATGTCGAGAGGTGTGA
1 AGGGTATGTCGAGAGGTGTGA
* * *
14976 AGGGTGTGTGGAGGGGTGT
1 AGGGTATGTCGAGAGGTGT
14995 CGAGAGAAAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.55, T:0.25
Consensus pattern (21 bp):
AGGGTATGTCGAGAGGTGTGA
Found at i:15926 original size:21 final size:21
Alignment explanation
Indices: 15900--15962 Score: 126
Period size: 21 Copynumber: 3.0 Consensus size: 21
15890 TAAGGAAGAA
15900 GTTTCAAGCTCATCGGAGTTG
1 GTTTCAAGCTCATCGGAGTTG
15921 GTTTCAAGCTCATCGGAGTTG
1 GTTTCAAGCTCATCGGAGTTG
15942 GTTTCAAGCTCATCGGAGTTG
1 GTTTCAAGCTCATCGGAGTTG
15963 CCTAAGATGC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.19, C:0.19, G:0.29, T:0.33
Consensus pattern (21 bp):
GTTTCAAGCTCATCGGAGTTG
Found at i:17555 original size:28 final size:28
Alignment explanation
Indices: 17512--17613 Score: 100
Period size: 28 Copynumber: 3.7 Consensus size: 28
17502 AAGTGAGCTT
* * * *
17512 AAAATGACCGAGATGCCCTTGAATGTGC
1 AAAATGACCAAAATGCCCCTGAACGTGC
*
17540 AAAATGACCAAAATGCCCCTGGACGTG-
1 AAAATGACCAAAATGCCCCTGAACGTGC
** * *
17567 TGAATGACAAAAATGCCCCTGAACATGC
1 AAAATGACCAAAATGCCCCTGAACGTGC
17595 -AAATGACCCAAAATGCCCC
1 AAAATGA-CCAAAATGCCCC
17614 CTAGATGACC
Statistics
Matches: 60, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
27 27 0.45
28 33 0.55
ACGTcount: A:0.37, C:0.26, G:0.20, T:0.17
Consensus pattern (28 bp):
AAAATGACCAAAATGCCCCTGAACGTGC
Found at i:27709 original size:26 final size:23
Alignment explanation
Indices: 27679--27725 Score: 67
Period size: 26 Copynumber: 1.9 Consensus size: 23
27669 CTTGAAAATT
27679 TGAAAAACTTTGATGGATGAGATGGA
1 TGAAAAAC-TTGAT-GAT-AGATGGA
27705 TGAAAAACTTGATGATAGATG
1 TGAAAAACTTGATGATAGATG
27726 AATCGAAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 3 0.14
25 5 0.24
26 8 0.38
ACGTcount: A:0.40, C:0.04, G:0.28, T:0.28
Consensus pattern (23 bp):
TGAAAAACTTGATGATAGATGGA
Found at i:39059 original size:2 final size:2
Alignment explanation
Indices: 39052--39081 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
39042 TATTTAGCCC
39052 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39082 GTATGTATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39086 original size:4 final size:4
Alignment explanation
Indices: 39079--39107 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
39069 TATATATATA
39079 TATG TATG TATG TATG TATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG TATG T
39108 TTCCTTCTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:39953 original size:51 final size:51
Alignment explanation
Indices: 39856--40002 Score: 131
Period size: 51 Copynumber: 2.9 Consensus size: 51
39846 AATTTAGATG
* * * * *
39856 AATTTGTAAATAAAGATTGAGTTTTTAATTAAAAGATTGAATCTTTTAAGT
1 AATTTGTAAATAAAGATTGAATGTTTAAGTAAAAGATTAAACCTTTTAAGT
* * * *
39907 AATTTGTAAATAAAGGTTGAATGTTTAAGTGAAAGGTTAAACCTTTTAATT
1 AATTTGTAAATAAAGATTGAATGTTTAAGTAAAAGATTAAACCTTTTAAGT
** * *
39958 AATGAG-AAATAAA-AATGAAATCTTTGAA-TAAAAGATTAAA-CTTTT
1 AATTTGTAAATAAAGATTG-AATGTTT-AAGTAAAAGATTAAACCTTTT
40003 GATTAAGGTG
Statistics
Matches: 78, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
49 7 0.09
50 23 0.29
51 48 0.62
ACGTcount: A:0.44, C:0.03, G:0.14, T:0.38
Consensus pattern (51 bp):
AATTTGTAAATAAAGATTGAATGTTTAAGTAAAAGATTAAACCTTTTAAGT
Found at i:40785 original size:41 final size:41
Alignment explanation
Indices: 40693--40889 Score: 245
Period size: 41 Copynumber: 4.7 Consensus size: 41
40683 TATTCCCAAA
** *
40693 TTGCCCTTCCTGGTCGGAAGGTGTTGTTTCAATGTCGTTTCCCTGT
1 TTGCCCTTCCCAGTCGGAAGGTGTTG-TTC-A---CGTTTCCCAGT
40739 TTGCCCTTCCCAGTCGGAAGGTGTTGTTCACGTTTCCCAGT
1 TTGCCCTTCCCAGTCGGAAGGTGTTGTTCACGTTTCCCAGT
* *
40780 TTGCCCTTCCCAGTCGGAAGGTGTTGTTTAC-TCTTTCCAGT
1 TTGCCCTTCCCAGTCGGAAGGTGTTGTTCACGT-TTCCCAGT
* * *
40821 TTGCCCTTCCCAGTCGGAAGGTGTTGTTTACTTTTCCTAGT
1 TTGCCCTTCCCAGTCGGAAGGTGTTGTTCACGTTTCCCAGT
40862 TTGCCCTTCCC-GTTCGGAAGGTGTTGTT
1 TTGCCCTTCCCAG-TCGGAAGGTGTTGTT
40890 TAGTTTCATC
Statistics
Matches: 141, Mismatches: 7, Indels: 11
0.89 0.04 0.07
Matches are distributed among these distances:
40 2 0.01
41 110 0.78
42 1 0.01
44 1 0.01
45 3 0.02
46 24 0.17
ACGTcount: A:0.11, C:0.26, G:0.24, T:0.39
Consensus pattern (41 bp):
TTGCCCTTCCCAGTCGGAAGGTGTTGTTCACGTTTCCCAGT
Found at i:40890 original size:41 final size:41
Alignment explanation
Indices: 40693--41587 Score: 251
Period size: 40 Copynumber: 21.3 Consensus size: 41
40683 TATTCCCAAA
** *
40693 TTGCCCTTCCTGGTCGGAAGGTGTTGTTTCAATGTCGTTTCCCT-GT
1 TTGCCCTTCCCAGTCGGAAGGTGTTGTTT--A---C-TTTTCCTAGT
* * *
40739 TTGCCCTTCCCAGTCGGAAGGTGTTGTTCACGTTTCCCAGT
1 TTGCCCTTCCCAGTCGGAAGGTGTTGTTTACTTTTCCTAGT
40780 TTGCCCTTCCCAGTCGGAAGGTGTTGTTTACTCTTTCC-AGT
1 TTGCCCTTCCCAGTCGGAAGGTGTTGTTTACT-TTTCCTAGT
40821 TTGCCCTTCCCAGTCGGAAGGTGTTGTTTACTTTTCCTAGT
1 TTGCCCTTCCCAGTCGGAAGGTGTTGTTTACTTTTCCTAGT
* * *
40862 TTGCCCTTCCC-GTTCGGAAGGTGTTGTTTAGTTTCATCTTATTCCCGG
1 TTGCCCTTCCCAG-TCGGAAGGTGTTGTTTACTTT--TCCTA-----GT
* * *
40910 TTGCCGTTCCCCA-TCGGAAGGTGTTGTTGAATTCGTCTTATTCCCAGT
1 TTGCCCTT-CCCAGTCGGAAGGTGTTG-T---TT--ACTT-TTCCTAGT
* *
40958 TTGCCCTTCCCGGTCGGAAGGTGTTGTTTAGTTTCGTCCTATTCCCAGT
1 TTGCCCTTCCCAGTCGGAAGGTGTTGTTTA----C-T--T-TTCCTAGT
** * * *
41007 TTGCCCCACCCCA-CCGGAAGTTGTTATTT--TTATTCCT-GTT
1 TTG-CCCTTCCCAGTCGGAAGGTGTTGTTTACTT-TTCCTAG-T
* **
41047 TTGCCCTTCCCCA-CCGGAAGGTGTTGTTTACCTTTTCAC-AAA
1 TTGCCCTT-CCCAGTCGGAAGGTGTTGTTTA-CTTTTC-CTAGT
*
41089 TTGCCCTTCCTCA-TCGGAAGTTGTTGTTTAAGCCTGCTTTTCCCT-GTT
1 TTGCCCTTCC-CAGTCGGAAGGTGTTGTTT-A-----CTTTT-CCTAG-T
* *
41137 TTGCCCTTCCCCA-CCGGAAGGTGTTGTTT--TAATTCCT-GTT
1 TTGCCCTT-CCCAGTCGGAAGGTGTTGTTTACT-TTTCCTAG-T
* * ** * *
41177 TTGTCGTTCCC-CCCTGGAAGATGTTGTTT--TAATTCCT-GTT
1 TTGCCCTTCCCAGTC-GGAAGGTGTTGTTTACT-TTTCCTAG-T
* * * * * *
41217 TTACCCTTCCCCA-CCGGAAGATGTTGTTT--TATTCGTATT
1 TTGCCCTT-CCCAGTCGGAAGGTGTTGTTTACTTTTCCTAGT
* * * * * *
41256 TTGCCCTTCGTC--TCCGGATGGTGTTGTTTTC-ATTCCCATT
1 TTGCCCTTC-CCAGT-CGGAAGGTGTTGTTTACTTTTCCTAGT
* *
41296 TTGCCCTTCCCCA-CCGGAAGGTATTGTTTACTTTTCCT-GTT
1 TTGCCCTT-CCCAGTCGGAAGGTGTTGTTTACTTTTCCTAG-T
* * * * * *
41337 TTGCCCTTTCCCACT-GGAAGGTGTAG-TTCCTATTCTTATT
1 TTGCCC-TTCCCAGTCGGAAGGTGTTGTTTACTTTTCCTAGT
* * * *
41377 TTGCCCTTCCCCA-TCGGAATGTGTTGTTTTC-ATT-CTTGTT
1 TTGCCCTT-CCCAGTCGGAAGGTGTTGTTTACTTTTCCTAG-T
* * ** *
41417 TTGCCCTTCCCCA-CCGGAAGTTGTTGTTTA-AATTCCCAGT
1 TTGCCCTT-CCCAGTCGGAAGGTGTTGTTTACTTTTCCTAGT
* *
41457 TTGCCCTTCCCCA-CCGGAAGGTATTGTTT--TTATTCCT-GTT
1 TTGCCCTT-CCCAGTCGGAAGGTGTTGTTTACTT-TTCCTAG-T
* * * *
41497 TTGGCCTTCCCCA-CCAGAAGGTGTTGTTTA-TGTTCCT-GT
1 TTGCCCTT-CCCAGTCGGAAGGTGTTGTTTACTTTTCCTAGT
* *
41536 TCTGCCCTTCCCCA-CCGGAAGGTGTTGTTT-CTGTTCCT-GT
1 T-TGCCCTT-CCCAGTCGGAAGGTGTTGTTTACTTTTCCTAGT
41576 TATGCCCTTCCC
1 T-TGCCCTTCCC
41588 CACCAAAAGG
Statistics
Matches: 680, Mismatches: 95, Indels: 155
0.73 0.10 0.17
Matches are distributed among these distances:
38 1 0.00
39 46 0.07
40 294 0.43
41 142 0.21
42 35 0.05
43 8 0.01
44 3 0.00
46 27 0.04
47 11 0.02
48 67 0.10
49 32 0.05
50 6 0.01
52 2 0.00
53 3 0.00
54 2 0.00
55 1 0.00
ACGTcount: A:0.12, C:0.27, G:0.20, T:0.40
Consensus pattern (41 bp):
TTGCCCTTCCCAGTCGGAAGGTGTTGTTTACTTTTCCTAGT
Found at i:40980 original size:96 final size:87
Alignment explanation
Indices: 40693--41012 Score: 314
Period size: 82 Copynumber: 3.6 Consensus size: 87
40683 TATTCCCAAA
* * * * *
40693 TTGCCCTTCCTGGTCGGAAGGTGTTGTTTCAATGTC-GT-TTCCCTGTTTGCCCTTCCCAGTCGG
1 TTGCCCTTCCCGGTCGGAAGGTGTTGTTT-AGTTTCTCTATTCCC-GGTTGCCCTTCCCAGTCGG
* *
40756 AAGGTGTTGTTCACGTTTCCCAGT
64 AAGGTGTTGTTTACTTTTCCCAGT
* * *
40780 TTGCCCTTCCCAGTCGGAAGGTGTTGTTTA----CTCT-TTCCAGTTTGCCCTTCCCAGTCGGAA
1 TTGCCCTTCCCGGTCGGAAGGTGTTGTTTAGTTTCTCTATTCCCGGTTGCCCTTCCCAGTCGGAA
*
40840 GGTGTTGTTTACTTTTCCTAGT
66 GGTGTTGTTTACTTTTCCCAGT
* *
40862 TTGCCCTTCCCGTTCGGAAGGTGTTGTTTAGTTTCATCTTATTCCCGGTTGCCGTTCCCCA-TCG
1 TTGCCCTTCCCGGTCGGAAGGTGTTGTTTAGTTTC-TC-TATTCCCGGTTGCCCTT-CCCAGTCG
*
40926 GAAGGTGTTGTTGAATTCGTCTTATTCCCAGT
63 GAAGGTGTTG-T---TT--ACTT-TTCCCAGT
*
40958 TTGCCCTTCCCGGTCGGAAGGTGTTGTTTAGTTTCGTCCTATTCCCAGTTTGCCC
1 TTGCCCTTCCCGGTCGGAAGGTGTTGTTTAGTTTC-T-CTATTCCC-GGTTGCCC
41013 CACCCCACCG
Statistics
Matches: 197, Mismatches: 18, Indels: 26
0.82 0.07 0.11
Matches are distributed among these distances:
82 69 0.35
83 5 0.03
86 2 0.01
87 29 0.15
88 1 0.01
89 25 0.13
90 5 0.03
93 2 0.01
95 3 0.02
96 49 0.25
97 7 0.04
ACGTcount: A:0.11, C:0.26, G:0.23, T:0.39
Consensus pattern (87 bp):
TTGCCCTTCCCGGTCGGAAGGTGTTGTTTAGTTTCTCTATTCCCGGTTGCCCTTCCCAGTCGGAA
GGTGTTGTTTACTTTTCCCAGT
Found at i:41025 original size:49 final size:49
Alignment explanation
Indices: 40854--41165 Score: 218
Period size: 48 Copynumber: 6.8 Consensus size: 49
40844 TTGTTTACTT
* ** *
40854 TTCCTAGTTTGCCCTTCCCGTTCGGAAGGTGTTGTTTAGTTTCATCTTA
1 TTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAGTTTCGTCTTA
* * * *
40903 TTCCC-GGTTGCCGTTCCCCATCGGAAGGTGTTGTTGA-ATTCGTCTTA
1 TTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAGTTTCGTCTTA
** *
40950 TTCCCAGTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTAGTTTCGTCCTA
1 TTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAGTTTCGTCTTA
** *
40999 TTCCCAGTTTGCCCCACCCCACCGGAA---GTTG-TTA--TT--T-TTA
1 TTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAGTTTCGTCTTA
* *
41039 TT-CCTGTTTTGCCCTTCCCCACCGGAAGGTGTTGTTTA----C--CTT-
1 TTCCCAG-TTTGCCCTTCCCCATCGGAAGGTGTTGTTTAGTTTCGTCTTA
* ** * * **
41081 TTCACAAATTGCCCTTCCTCATCGGAAGTTGTTGTTTAAGCCT-G-CTT-
1 TTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTT-AGTTTCGTCTTA
* *
41128 TTCCCTGTTTTGCCCTTCCCCACCGGAAGGTGTTGTTT
1 TTCCCAG-TTTGCCCTTCCCCATCGGAAGGTGTTGTTT
41166 TAATTCCTGT
Statistics
Matches: 208, Mismatches: 38, Indels: 35
0.74 0.14 0.12
Matches are distributed among these distances:
39 3 0.01
40 22 0.11
41 1 0.00
42 28 0.13
43 10 0.05
44 3 0.01
45 3 0.01
46 4 0.02
47 20 0.10
48 80 0.38
49 34 0.16
ACGTcount: A:0.13, C:0.28, G:0.21, T:0.39
Consensus pattern (49 bp):
TTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAGTTTCGTCTTA
Found at i:41052 original size:40 final size:40
Alignment explanation
Indices: 41006--41624 Score: 534
Period size: 40 Copynumber: 15.3 Consensus size: 40
40996 CTATTCCCAG
** * *
41006 TTTGCCCCACCCCACCGGAAGTTGTTATTTTTATTCCTGT
1 TTTGCCCTTCCCCACCGGAAGGTGTTGTTTTTATTCCTGT
**
41046 TTTGCCCTTCCCCACCGGAAGGTGTTGTTTACCTT-TTCAC-AA
1 TTTGCCCTTCCCCACCGGAAGGTGTTGTTT---TTATTC-CTGT
* * * * *
41088 ATTGCCCTTCCTCATCGGAAGTTGTTGTTTAAGCCTGCTTTTCCCTGT
1 TTTGCCCTTCCCCACCGGAAGGTGTTGTTT-----T--TATT-CCTGT
*
41136 TTTGCCCTTCCCCACCGGAAGGTGTTGTTTTAATTCCTGT
1 TTTGCCCTTCCCCACCGGAAGGTGTTGTTTTTATTCCTGT
* * * *
41176 TTTGTCGTTCCCC-CCTGGAAGATGTTGTTTTAATTCCTGT
1 TTTGCCCTTCCCCACC-GGAAGGTGTTGTTTTTATTCCTGT
* * * *
41216 TTTACCCTTCCCCACCGGAAGATGTTG-TTTTATTCGTAT
1 TTTGCCCTTCCCCACCGGAAGGTGTTGTTTTTATTCCTGT
** * * * **
41255 TTTGCCCTTCGTCTCCGGATGGTGTTGTTTTCATTCCCAT
1 TTTGCCCTTCCCCACCGGAAGGTGTTGTTTTTATTCCTGT
*
41295 TTTGCCCTTCCCCACCGGAAGGTATTGTTTACTT-TTCCTGT
1 TTTGCCCTTCCCCACCGGAAGGTGTTGTTT--TTATTCCTGT
* * * ** * *
41336 TTTGCCCTTTCCCACTGGAAGGTGTAGTTCCTATTCTTAT
1 TTTGCCCTTCCCCACCGGAAGGTGTTGTTTTTATTCCTGT
* * * *
41376 TTTGCCCTTCCCCATCGGAATGTGTTGTTTTCATTCTTGT
1 TTTGCCCTTCCCCACCGGAAGGTGTTGTTTTTATTCCTGT
* ** *
41416 TTTGCCCTTCCCCACCGGAAGTTGTTGTTTAAATTCCCAG-
1 TTTGCCCTTCCCCACCGGAAGGTGTTGTTTTTATT-CCTGT
*
41456 TTTGCCCTTCCCCACCGGAAGGTATTGTTTTTATTCCTGT
1 TTTGCCCTTCCCCACCGGAAGGTGTTGTTTTTATTCCTGT
* * * *
41496 TTTGGCCTTCCCCACCAGAAGGTGTTGTTTATGTTCCTGT
1 TTTGCCCTTCCCCACCGGAAGGTGTTGTTTTTATTCCTGT
* * *
41536 TCTGCCCTTCCCCACCGGAAGGTGTTGTTTCTGTTCCTGT
1 TTTGCCCTTCCCCACCGGAAGGTGTTGTTTTTATTCCTGT
* ** *
41576 TATGCCCTTCCCCACCAAAAGGTTTTG-TTTTATTCCTG-
1 TTTGCCCTTCCCCACCGGAAGGTGTTGTTTTTATTCCTGT
*
41614 TCTGCCCTTCC
1 TTTGCCCTTCC
41625 TGATGCGCCA
Statistics
Matches: 470, Mismatches: 90, Indels: 40
0.78 0.15 0.07
Matches are distributed among these distances:
38 10 0.02
39 45 0.10
40 311 0.66
41 36 0.08
42 30 0.06
43 4 0.01
44 3 0.01
46 1 0.00
47 3 0.01
48 27 0.06
ACGTcount: A:0.13, C:0.28, G:0.18, T:0.41
Consensus pattern (40 bp):
TTTGCCCTTCCCCACCGGAAGGTGTTGTTTTTATTCCTGT
Found at i:42634 original size:40 final size:40
Alignment explanation
Indices: 42569--42753 Score: 194
Period size: 40 Copynumber: 4.6 Consensus size: 40
42559 ATTCGTATCA
*
42569 CTTCCCCACTGGAAGGTGTTGTTTTAATTCCCGTTTTGCC
1 CTTCCCCACCGGAAGGTGTTGTTTTAATTCCCGTTTTGCC
*
42609 CTTCTCCACCGGAAGGTGTTGTTTTAATTCCCGTTTTGCC
1 CTTCCCCACCGGAAGGTGTTGTTTTAATTCCCGTTTTGCC
* * * ** *
42649 CTTCCCCATCGGAAGGCGTTGTTTTCATTCATGTTTTGTC
1 CTTCCCCACCGGAAGGTGTTGTTTTAATTCCCGTTTTGCC
* * * * * *
42689 CTTCCCCACCTGAATGTGTCG-TTTACTTTTCCCAG-CTCGCC
1 CTTCCCCACCGGAAGGTGTTGTTTTA--ATTCCC-GTTTTGCC
*
42730 CTTCCCCATCGGAAGGTGTTGTTT
1 CTTCCCCACCGGAAGGTGTTGTTT
42754 GCTTTTCCTA
Statistics
Matches: 116, Mismatches: 25, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
39 3 0.03
40 87 0.75
41 23 0.20
42 3 0.03
ACGTcount: A:0.12, C:0.29, G:0.19, T:0.39
Consensus pattern (40 bp):
CTTCCCCACCGGAAGGTGTTGTTTTAATTCCCGTTTTGCC
Found at i:43317 original size:23 final size:23
Alignment explanation
Indices: 43291--43370 Score: 63
Period size: 23 Copynumber: 3.3 Consensus size: 23
43281 TTACAACTTG
43291 CCCGGAGGCTACCAGAATTACTA
1 CCCGGAGGCTACCAGAATTACTA
* * **
43314 CCCGGAGG-TTCCTGATATTGTACCCG
1 CCCGGAGGCTACCAGA-A-T-TA-CTA
* *
43340 CCCGGAAGCTACCAGAATTGCTA
1 CCCGGAGGCTACCAGAATTACTA
43363 CCCGGAGG
1 CCCGGAGG
43371 TTTCTGACTT
Statistics
Matches: 41, Mismatches: 11, Indels: 10
0.66 0.18 0.16
Matches are distributed among these distances:
22 5 0.12
23 17 0.41
24 2 0.05
25 3 0.07
26 9 0.22
27 5 0.12
ACGTcount: A:0.24, C:0.31, G:0.26, T:0.19
Consensus pattern (23 bp):
CCCGGAGGCTACCAGAATTACTA
Found at i:47465 original size:16 final size:16
Alignment explanation
Indices: 47440--47470 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
47430 TAAATGAAAT
47440 ATTTTGTGCTTTTTTC
1 ATTTTGTGCTTTTTTC
*
47456 ATTTTTTGCTTTTTT
1 ATTTTGTGCTTTTTT
47471 TTTGTAATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.06, C:0.10, G:0.10, T:0.74
Consensus pattern (16 bp):
ATTTTGTGCTTTTTTC
Found at i:48009 original size:50 final size:50
Alignment explanation
Indices: 47870--48085 Score: 202
Period size: 50 Copynumber: 4.3 Consensus size: 50
47860 ATTTCTGGGT
* * * ** *
47870 GGATCGTCTTCCGATCAGCTTCTTTGAACTATCTTCTGATTCAA--ATATAAA
1 GGATCGTCTTCCGCTTA--TTCTTCGAACTATCTTCCAATTCAATCTTA-AAA
* * * *
47921 GGATAGTCTTCCGATCAACTTCTTCAAACTATCTTCCAATTCAATCTTAAAA
1 GGATCGTCTTCCGCT-TA-TTCTTCGAACTATCTTCCAATTCAATCTTAAAA
* * * *
47973 GGATTGTCTTCCTCTTATTCTTCGAACTGTCTTCCAATTTAATCTTAAAA
1 GGATCGTCTTCCGCTTATTCTTCGAACTATCTTCCAATTCAATCTTAAAA
* * * * *
48023 GGACCATCTTCCGCTTATCCTTCGAATTATCTTCCAATTCAGTCTTAAAA
1 GGATCGTCTTCCGCTTATTCTTCGAACTATCTTCCAATTCAATCTTAAAA
48073 GGATCGTCTTCCG
1 GGATCGTCTTCCG
48086 AACCATTTTT
Statistics
Matches: 137, Mismatches: 25, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
50 82 0.60
51 37 0.27
52 16 0.12
53 2 0.01
ACGTcount: A:0.26, C:0.25, G:0.12, T:0.38
Consensus pattern (50 bp):
GGATCGTCTTCCGCTTATTCTTCGAACTATCTTCCAATTCAATCTTAAAA
Found at i:48104 original size:27 final size:27
Alignment explanation
Indices: 48074--48266 Score: 287
Period size: 27 Copynumber: 7.1 Consensus size: 27
48064 GTCTTAAAAG
*
48074 GATCGTCTTCCGAACCATTTTTGATGA
1 GATCGTCTTCCGAACCATTTCTGATGA
*
48101 GATCGTCTTCCGAACCATTTATGATGA
1 GATCGTCTTCCGAACCATTTCTGATGA
*
48128 GATCGTCTTCCGAACCATTTATGATGA
1 GATCGTCTTCCGAACCATTTCTGATGA
* *
48155 GATCGTCTTCCAAACTATTTCTGATGA
1 GATCGTCTTCCGAACCATTTCTGATGA
*
48182 GATCGTCTTCCGAATCATTTCTGATGA
1 GATCGTCTTCCGAACCATTTCTGATGA
* **
48209 GATCGTCTTCCAAATTATTTCTGATGA
1 GATCGTCTTCCGAACCATTTCTGATGA
**
48236 GATCGTCTTCAAAACCATTTCTGATGA
1 GATCGTCTTCCGAACCATTTCTGATGA
48263 GATC
1 GATC
48267 AATTTCTAAA
Statistics
Matches: 154, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 154 1.00
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.36
Consensus pattern (27 bp):
GATCGTCTTCCGAACCATTTCTGATGA
Found at i:48313 original size:40 final size:40
Alignment explanation
Indices: 48268--48377 Score: 123
Period size: 41 Copynumber: 2.7 Consensus size: 40
48258 GATGAGATCA
* *
48268 ATTTCTAAATAACCATCTTTTGATTGACTTTTGAAAATCT
1 ATTTCTAAATAACCATCTTTTGATTGACTTCTGAAAATCC
* *
48308 ATTTCTAAAATAACCATCTTCTAATT-AGCTTCTGAAAATCC
1 ATTTCT-AAATAACCATCTTTTGATTGA-CTTCTGAAAATCC
* * * *
48349 ATTTCTAACTAACCAACTTTCGATGGACT
1 ATTTCTAAATAACCATCTTTTGATTGACT
48378 GCTTAGAATC
Statistics
Matches: 57, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
40 22 0.39
41 35 0.61
ACGTcount: A:0.34, C:0.20, G:0.07, T:0.39
Consensus pattern (40 bp):
ATTTCTAAATAACCATCTTTTGATTGACTTCTGAAAATCC
Found at i:53222 original size:2 final size:2
Alignment explanation
Indices: 53215--53241 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
53205 AAGCAAACAG
53215 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
53242 CATGGAAAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:59362 original size:16 final size:16
Alignment explanation
Indices: 59337--59369 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
59327 GAGAACATGA
*
59337 TTTGAGAAAAACCTTT
1 TTTGAAAAAAACCTTT
59353 TTTGAAAAAAACCTTT
1 TTTGAAAAAAACCTTT
59369 T
1 T
59370 ATTACCTCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.39
Consensus pattern (16 bp):
TTTGAAAAAAACCTTT
Found at i:59412 original size:20 final size:20
Alignment explanation
Indices: 59384--59424 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
59374 CCTCTTTTGA
59384 TTTTCTGATTTT-TTCTCTTT
1 TTTTCTGATTTTCTTCT-TTT
*
59404 TTTTTTGATTTTCTTCTTTT
1 TTTTCTGATTTTCTTCTTTT
59424 T
1 T
59425 CTATCTCTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.05, C:0.12, G:0.05, T:0.78
Consensus pattern (20 bp):
TTTTCTGATTTTCTTCTTTT
Found at i:67696 original size:1 final size:1
Alignment explanation
Indices: 67690--67717 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
67680 TGAGTAGGAA
67690 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
67718 GGTGCAGCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Done.