Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015525.1 Corchorus olitorius cultivar O-4 contig15558, 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: 35855
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Found at i:636 original size:22 final size:22
Alignment explanation
Indices: 606--751 Score: 132
Period size: 22 Copynumber: 6.6 Consensus size: 22
596 TCCAACGTAG
*
606 AAATATTGATAACCACACTGCGA
1 AAAT-TTGATAACCACACTGTGA
* *
629 AAATTTGATAACCTCATTGTG-
1 AAATTTGATAACCACACTGTGA
* * *
650 AAATTTCGATAACCTCCCTATGA
1 AAATTT-GATAACCACACTGTGA
*
673 AAATTTGATAACCACAATGTGA
1 AAATTTGATAACCACACTGTGA
* *
695 AATTTTGATAACCACACTATGA
1 AAATTTGATAACCACACTGTGA
** **
717 AGTTTTGATAACCACACAATGA
1 AAATTTGATAACCACACTGTGA
**
739 AGTTTTGATAACC
1 AAATTTGATAACC
752 TCATTGTCTA
Statistics
Matches: 106, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
21 6 0.06
22 90 0.85
23 10 0.09
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.30
Consensus pattern (22 bp):
AAATTTGATAACCACACTGTGA
Found at i:739 original size:66 final size:66
Alignment explanation
Indices: 606--751 Score: 166
Period size: 66 Copynumber: 2.2 Consensus size: 66
596 TCCAACGTAG
* * * * * * *
606 AAATATTGATAACCACACTGCGAAAATTTGATAACCTCATTGTGAAATTTCGATAACCTCCCTAT
1 AAAT-TTGATAACCACAATGCGAAAATTTGATAACCACACTATGAAATTTCGATAACCACACAAT
671 GA
65 GA
* * * *
673 AAATTTGATAACCACAATGTGAAATTTTGATAACCACACTATGAAGTTTTGATAACCACACAATG
1 AAATTTGATAACCACAATGCGAAAATTTGATAACCACACTATGAAATTTCGATAACCACACAATG
738 A
66 A
**
739 AGTTTTGATAACC
1 AAATTTGATAACC
752 TCATTGTCTA
Statistics
Matches: 66, Mismatches: 13, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
66 62 0.94
67 4 0.06
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.30
Consensus pattern (66 bp):
AAATTTGATAACCACAATGCGAAAATTTGATAACCACACTATGAAATTTCGATAACCACACAATG
A
Found at i:745 original size:44 final size:43
Alignment explanation
Indices: 605--751 Score: 159
Period size: 44 Copynumber: 3.3 Consensus size: 43
595 CTCCAACGTA
* ** * *
605 GAAATATTGATAACCACACTGCGAAAATTTGATAACCTCATTGT
1 GAAATTTTGATAACCACACTATGAAAATTTGATAACCACA-AGT
* * *
649 GAAATTTCGATAACCTCCCTATGAAAATTTGATAACCACAATGT
1 GAAATTTTGATAACCACACTATGAAAATTTGATAACCACAA-GT
** *
693 GAAATTTTGATAACCACACTATGAAGTTTTGATAACCACACAAT
1 GAAATTTTGATAACCACACTATGAAAATTTGATAACCACA-AGT
*
737 GAAGTTTTGATAACC
1 GAAATTTTGATAACC
752 TCATTGTCTA
Statistics
Matches: 86, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
44 85 0.99
45 1 0.01
ACGTcount: A:0.39, C:0.18, G:0.13, T:0.30
Consensus pattern (43 bp):
GAAATTTTGATAACCACACTATGAAAATTTGATAACCACAAGT
Found at i:896 original size:22 final size:22
Alignment explanation
Indices: 871--937 Score: 57
Period size: 22 Copynumber: 3.0 Consensus size: 22
861 TTGTGATATT
871 CTCTATATGTAATTTTGATAAC
1 CTCTATATGTAATTTTGATAAC
* *
893 CTCTCCATA-AT-ATTTTCATAAC
1 CTCT--ATATGTAATTTTGATAAC
* * *
915 CTCTCTATGAAATTTTGTTAAC
1 CTCTATATGTAATTTTGATAAC
937 C
1 C
938 ATCCTAGGAA
Statistics
Matches: 34, Mismatches: 7, Indels: 8
0.69 0.14 0.16
Matches are distributed among these distances:
20 2 0.06
22 28 0.82
23 1 0.03
24 3 0.09
ACGTcount: A:0.30, C:0.21, G:0.06, T:0.43
Consensus pattern (22 bp):
CTCTATATGTAATTTTGATAAC
Found at i:1064 original size:22 final size:22
Alignment explanation
Indices: 978--1216 Score: 127
Period size: 22 Copynumber: 10.8 Consensus size: 22
968 TGATAACCTC
* *
978 CCTTTCTATGAAATTTTGTTAA
1 CCTTCCTATGAAATTTTGATAA
* *
1000 CGTT-CTAAT-TAATTTTGATAA
1 CCTTCCT-ATGAAATTTTGATAA
* * **
1021 CC-ACACTATAAAATTTCAATAA
1 CCTTC-CTATGAAATTTTGATAA
*
1043 CCTTCGTATGAAATTTTGATAA
1 CCTTCCTATGAAATTTTGATAA
* * *
1065 TC-TCCATAAGAGATTTTGATAA
1 CCTTCC-TATGAAATTTTGATAA
** *
1087 CCTTTTTTTATGAAATTTTGGTAA
1 CC--TTCCTATGAAATTTTGATAA
*
1111 CC-TCTGTATGAAATTTTGATAA
1 CCTTC-CTATGAAATTTTGATAA
* *
1133 --TTACACTACGAAGTTTTGATAA
1 CCTT-C-CTATGAAATTTTGATAA
*
1155 CC-TCCATATGAAATTTTGGTAA
1 CCTTCC-TATGAAATTTTGATAA
* *
1177 CC-ACACTATGAAATTTTAATAA
1 CCTTC-CTATGAAATTTTGATAA
*
1199 CCTTCCTATGTAATTTTG
1 CCTTCCTATGAAATTTTG
1217 TTTTGATTGT
Statistics
Matches: 161, Mismatches: 39, Indels: 34
0.69 0.17 0.15
Matches are distributed among these distances:
21 20 0.12
22 121 0.75
23 4 0.02
24 15 0.09
25 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.41
Consensus pattern (22 bp):
CCTTCCTATGAAATTTTGATAA
Found at i:1150 original size:68 final size:66
Alignment explanation
Indices: 1040--1198 Score: 171
Period size: 68 Copynumber: 2.4 Consensus size: 66
1030 AAAATTTCAA
* ***
1040 TAACCT-TCGTATGAAATTTTGATAATCTCCATAAGAGATTTTGATAACCTTTTTTTATGAAATT
1 TAACCTCT-GTATGAAATTTTGATAATCTACATAAGAGATTTTGATAACC--TCCATATGAAATT
1104 TTGG
63 TTGG
*
1108 TAACCTCTGTATGAAATTTTGATAAT-TACACTACGA-AGTTTTGATAACCTCCATATGAAATTT
1 TAACCTCTGTATGAAATTTTGATAATCTACA-TAAGAGA-TTTTGATAACCTCCATATGAAATTT
1171 TGG
64 TGG
* ** *
1174 TAACCACACTATGAAATTTTAATAA
1 TAACCTCTGTATGAAATTTTGATAA
1199 CCTTCCTATG
Statistics
Matches: 79, Mismatches: 9, Indels: 8
0.82 0.09 0.08
Matches are distributed among these distances:
66 35 0.44
67 4 0.05
68 39 0.49
69 1 0.01
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.40
Consensus pattern (66 bp):
TAACCTCTGTATGAAATTTTGATAATCTACATAAGAGATTTTGATAACCTCCATATGAAATTTTG
G
Found at i:3146 original size:21 final size:22
Alignment explanation
Indices: 3120--3177 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 22
3110 CACACTAAAT
* *
3120 AAAA-TTGGTAACCACACTATG
1 AAAATTTGATAACCACACCATG
3141 AAAATTTTGATAACCACACCATG
1 AAAA-TTTGATAACCACACCATG
3164 -AAATTTCGATAACC
1 AAAATTT-GATAACC
3178 TCCCTATGAG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
21 7 0.22
22 10 0.31
23 15 0.47
ACGTcount: A:0.43, C:0.21, G:0.10, T:0.26
Consensus pattern (22 bp):
AAAATTTGATAACCACACCATG
Found at i:3332 original size:48 final size:48
Alignment explanation
Indices: 3248--3340 Score: 125
Period size: 48 Copynumber: 1.9 Consensus size: 48
3238 ATTTTCATAA
* *
3248 CCTCCCTATAAAATTTTGTTAACCTCTAGCACAAATTTTGGTAACCTC
1 CCTCCCTATAAAATTTTGGTAACCTCTAGCACAAATTTTGATAACCTC
* * *
3296 CCTCCCTATGAAATTTTGGTAACCTCT-GTATGAAATTTTGATAAC
1 CCTCCCTATAAAATTTTGGTAACCTCTAGCA-CAAATTTTGATAAC
3341 TACACTATGA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
47 2 0.05
48 37 0.95
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.37
Consensus pattern (48 bp):
CCTCCCTATAAAATTTTGGTAACCTCTAGCACAAATTTTGATAACCTC
Found at i:3349 original size:22 final size:22
Alignment explanation
Indices: 2943--3423 Score: 206
Period size: 22 Copynumber: 21.4 Consensus size: 22
2933 TTCCAATGTA
* * * *
2943 GAAATATTGATAACCACATTTT
1 GAAATTTTGATAACCTCACTAT
*
2965 GCAAA-TTTGATAAGCTCA-TAT
1 G-AAATTTTGATAACCTCACTAT
* *
2986 GAAATTTCGATAACCTCCCTAT
1 GAAATTTTGATAACCTCACTAT
* * *
3008 GAAAATTTGATAACCACACTGT
1 GAAATTTTGATAACCTCACTAT
* * *
3030 GAAATTTGGGTAACCACACTAT
1 GAAATTTTGATAACCTCACTAT
* * *
3052 GAAATTTCGATAACCTCAGTGT
1 GAAATTTTGATAACCTCACTAT
* *
3074 GAAATTTTGGTAATCTGC-CTAT
1 GAAATTTTGATAACCT-CACTAT
* * * *
3096 AAAATTTTAATAATCACACTAAAT
1 GAAATTTTGATAACCTCACT--AT
* * *
3120 -AAA-ATTGGTAACCACACTAT
1 GAAATTTTGATAACCTCACTAT
* *
3140 GAAAATTTTGATAACCACACCAT
1 G-AAATTTTGATAACCTCACTAT
* *
3163 GAAATTTCGATAACCTCCCTAT
1 GAAATTTTGATAACCTCACTAT
* * **
3185 GAGAATGAAACTGTGATATCCTCTTTAT
1 GA-AAT-----TTTGATAACCTCACTAT
* * * *
3213 GTATTTTTGATAACCTCTCCAT
1 GAAATTTTGATAACCTCACTAT
* * *
3235 AAAATTTTCATAACCTCCCTAT
1 GAAATTTTGATAACCTCACTAT
* *
3257 AAAATTTTGTTAACCTCTAGC-A-
1 GAAATTTTGATAACCTC-A-CTAT
* * *
3279 CAAATTTTGGTAACCTCCCTCCCTAT
1 GAAATTTTGATAA----CCTCACTAT
* **
3305 GAAATTTTGGTAACCTCTGTAT
1 GAAATTTTGATAACCTCACTAT
3327 GAAATTTTGATAA-CTACACTAT
1 GAAATTTTGATAACCT-CACTAT
* *
3349 GAAGTTTTGATAATCTCTA-TAT
1 GAAATTTTGATAACCTC-ACTAT
* * * *
3371 GAAATATTGGTAACCACACTAC
1 GAAATTTTGATAACCTCACTAT
* **
3393 GAAATTTTGATAATCTTTCTAT
1 GAAATTTTGATAACCTCACTAT
*
3415 GTAATTTTG
1 GAAATTTTG
3424 GTTTGATTGT
Statistics
Matches: 346, Mismatches: 85, Indels: 56
0.71 0.17 0.11
Matches are distributed among these distances:
20 5 0.01
21 17 0.05
22 259 0.75
23 29 0.08
24 4 0.01
25 1 0.00
26 16 0.05
27 2 0.01
28 13 0.04
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.35
Consensus pattern (22 bp):
GAAATTTTGATAACCTCACTAT
Found at i:4202 original size:6 final size:6
Alignment explanation
Indices: 4191--4242 Score: 72
Period size: 6 Copynumber: 8.7 Consensus size: 6
4181 AATTACGTTC
4191 TTTTGT TTTTGT TTTTGAT TTTTGT TTTTGT TTTT-T GTTTTGT TTTT-T
1 TTTTGT TTTTGT TTTTG-T TTTTGT TTTTGT TTTTGT -TTTTGT TTTTGT
4239 TTTT
1 TTTT
4243 ATGAAAGCTA
Statistics
Matches: 43, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
5 6 0.14
6 30 0.70
7 7 0.16
ACGTcount: A:0.02, C:0.00, G:0.13, T:0.85
Consensus pattern (6 bp):
TTTTGT
Found at i:4215 original size:19 final size:18
Alignment explanation
Indices: 4191--4242 Score: 72
Period size: 19 Copynumber: 2.9 Consensus size: 18
4181 AATTACGTTC
4191 TTTTGTTTTTG-TTTTTG
1 TTTTGTTTTTGTTTTTTG
4208 ATTTTTGTTTTTGTTTTTTG
1 --TTTTGTTTTTGTTTTTTG
4228 TTTTGTTTTT-TTTTT
1 TTTTGTTTTTGTTTTT
4243 ATGAAAGCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.16
18 10 0.31
19 11 0.34
20 6 0.19
ACGTcount: A:0.02, C:0.00, G:0.13, T:0.85
Consensus pattern (18 bp):
TTTTGTTTTTGTTTTTTG
Found at i:6029 original size:22 final size:23
Alignment explanation
Indices: 5982--6029 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 23
5972 CTAATCTATT
5982 TAAA-AATAAATAATTAAATTAA
1 TAAATAATAAATAATTAAATTAA
6004 -AAATAATAAAT-A-TATAATTAA
1 TAAATAATAAATAATTA-AATTAA
6025 TAAAT
1 TAAAT
6030 TATTGAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
20 2 0.09
21 10 0.43
22 11 0.48
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (23 bp):
TAAATAATAAATAATTAAATTAA
Found at i:6159 original size:21 final size:21
Alignment explanation
Indices: 6134--6175 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
6124 TATAATTTTA
* *
6134 TTTTATAGTAATGCCCTTAAT
1 TTTTATACTAATACCCTTAAT
6155 TTTTATACTAATACCCTTAAT
1 TTTTATACTAATACCCTTAAT
6176 GGTAATTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.31, C:0.17, G:0.05, T:0.48
Consensus pattern (21 bp):
TTTTATACTAATACCCTTAAT
Found at i:16736 original size:8 final size:8
Alignment explanation
Indices: 16718--16759 Score: 70
Period size: 8 Copynumber: 5.5 Consensus size: 8
16708 AAAATGAAAC
16718 AAAAACA-
1 AAAAACAG
16725 AAAAACAG
1 AAAAACAG
16733 AAAAACAG
1 AAAAACAG
16741 AAAAACAG
1 AAAAACAG
16749 AAAAAC-G
1 AAAAACAG
16756 AAAA
1 AAAA
16760 TTATGCCAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
7 12 0.35
8 22 0.65
ACGTcount: A:0.79, C:0.12, G:0.10, T:0.00
Consensus pattern (8 bp):
AAAAACAG
Found at i:16995 original size:25 final size:25
Alignment explanation
Indices: 16961--17059 Score: 171
Period size: 25 Copynumber: 4.0 Consensus size: 25
16951 CCAAACAATC
*
16961 TTGAGTACTCTCGCTCGGTCTCTAT
1 TTGAGCACTCTCGCTCGGTCTCTAT
* *
16986 TTGAGTACTCTCGTTCGGTCTCTAT
1 TTGAGCACTCTCGCTCGGTCTCTAT
17011 TTGAGCACTCTCGCTCGGTCTCTAT
1 TTGAGCACTCTCGCTCGGTCTCTAT
17036 TTGAGCACTCTCGCTCGGTCTCTA
1 TTGAGCACTCTCGCTCGGTCTCTA
17060 CAAACCAATC
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 71 1.00
ACGTcount: A:0.12, C:0.29, G:0.20, T:0.38
Consensus pattern (25 bp):
TTGAGCACTCTCGCTCGGTCTCTAT
Found at i:17085 original size:21 final size:21
Alignment explanation
Indices: 17056--17097 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
17046 TCGCTCGGTC
*
17056 TCTACAAACCAATC-ATCACA
1 TCTACAAACCAAACAATCACA
17076 TCTACCAAACCAAACAATCACA
1 TCTA-CAAACCAAACAATCACA
17098 CACACACCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 4 0.21
21 9 0.47
22 6 0.32
ACGTcount: A:0.48, C:0.36, G:0.00, T:0.17
Consensus pattern (21 bp):
TCTACAAACCAAACAATCACA
Found at i:17939 original size:25 final size:25
Alignment explanation
Indices: 17903--17951 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
17893 CCAAACAATC
*
17903 TTGAGCATTCTCGCTCGGTCTCTAT
1 TTGAGCACTCTCGCTCGGTCTCTAT
17928 TTGAGCACTCTCGCTCGGTCTCTA
1 TTGAGCACTCTCGCTCGGTCTCTA
17952 CAAACCAATC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.12, C:0.31, G:0.20, T:0.37
Consensus pattern (25 bp):
TTGAGCACTCTCGCTCGGTCTCTAT
Found at i:17976 original size:21 final size:21
Alignment explanation
Indices: 17948--17989 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
17938 TCGCTCGGTC
*
17948 TCTACAAACCAATC-ATCACA
1 TCTACAAACCAAACAATCACA
17968 TCTATCAAACCAAACAATCACA
1 TCTA-CAAACCAAACAATCACA
17990 CACACACACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 4 0.21
21 9 0.47
22 6 0.32
ACGTcount: A:0.48, C:0.33, G:0.00, T:0.19
Consensus pattern (21 bp):
TCTACAAACCAAACAATCACA
Found at i:18608 original size:31 final size:31
Alignment explanation
Indices: 18501--18677 Score: 140
Period size: 31 Copynumber: 5.6 Consensus size: 31
18491 ACGGTATCCG
*
18501 ACGTCGCATGCCACGTGTACCAAAAAGTGAC
1 ACGTGGCATGCCACGTGTACCAAAAAGTGAC
* * ** *
18532 ATGTGTCGCGTCACGTGTACCAAAAAGTGAC
1 ACGTGGCATGCCACGTGTACCAAAAAGTGAC
* ** ** *
18563 ATGTATCACACCATGTGTACCAAAAAGTGAC
1 ACGTGGCATGCCACGTGTACCAAAAAGTGAC
* **
18594 ACGTGGCATGCCATGTGTTTCAAAAAGTGAC
1 ACGTGGCATGCCACGTGTACCAAAAAGTGAC
* * *
18625 ACGTGACATGCCACGTGCA-CAAAGGATACGTGTCC
1 ACGTGGCATGCCACGTGTACCAAA--A-A-GTG-AC
18660 ACGTGGCATGCCACGTGT
1 ACGTGGCATGCCACGTGT
18678 CATTTTTGTC
Statistics
Matches: 116, Mismatches: 25, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
30 4 0.03
31 90 0.78
32 1 0.01
33 1 0.01
34 3 0.03
35 17 0.15
ACGTcount: A:0.30, C:0.25, G:0.24, T:0.21
Consensus pattern (31 bp):
ACGTGGCATGCCACGTGTACCAAAAAGTGAC
Found at i:20563 original size:32 final size:32
Alignment explanation
Indices: 20513--20595 Score: 87
Period size: 31 Copynumber: 2.6 Consensus size: 32
20503 TGCTGACGTG
* * *
20513 GCAATGCCACATCGGACCAAAAATGTCACGCA
1 GCAATGCCACGTCAGACCAAAAATGCCACGCA
* * **
20545 GCAATGCCACGTTAGACC-AATATGCCACGTG
1 GCAATGCCACGTCAGACCAAAAATGCCACGCA
*
20576 GCAAGGCCACGTCAGACCAA
1 GCAATGCCACGTCAGACCAA
20596 GGCGCTAACG
Statistics
Matches: 41, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
31 25 0.61
32 16 0.39
ACGTcount: A:0.34, C:0.31, G:0.22, T:0.13
Consensus pattern (32 bp):
GCAATGCCACGTCAGACCAAAAATGCCACGCA
Found at i:23941 original size:29 final size:29
Alignment explanation
Indices: 23883--23941 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
23873 ATATTTAAAT
** ** *
23883 GGAATTATATATATACTTTTTTTTTTGAA
1 GGAATTATATATATACTTAATTAATGGAA
23912 GGAATTATATATATACTTAATTAATGGAA
1 GGAATTATATATATACTTAATTAATGGAA
23941 G
1 G
23942 ATTGCTATCA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.37, C:0.03, G:0.14, T:0.46
Consensus pattern (29 bp):
GGAATTATATATATACTTAATTAATGGAA
Found at i:31933 original size:2 final size:2
Alignment explanation
Indices: 31926--31954 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
31916 TATACCAAGA
31926 AT 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 AT A
31955 ATTGAATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:32351 original size:14 final size:14
Alignment explanation
Indices: 32332--32362 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
32322 CCTTCTAATA
32332 TTACAAAGTTAAGT
1 TTACAAAGTTAAGT
32346 TTACAAAGTTAAGT
1 TTACAAAGTTAAGT
32360 TTA
1 TTA
32363 AATCCTTCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.42, C:0.06, G:0.13, T:0.39
Consensus pattern (14 bp):
TTACAAAGTTAAGT
Found at i:33711 original size:17 final size:18
Alignment explanation
Indices: 33678--33711 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
33668 TGTAATAGGT
*
33678 AAAATTATAATTGTATAA
1 AAAATGATAATTGTATAA
33696 AAAATGATAATT-TATA
1 AAAATGATAATTGTATA
33712 CTAATATGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (18 bp):
AAAATGATAATTGTATAA
Found at i:35089 original size:2 final size:2
Alignment explanation
Indices: 35082--35129 Score: 62
Period size: 2 Copynumber: 24.0 Consensus size: 2
35072 TTAAGCCCTT
* *
35082 TA TA TA TA -A TA TA TA TA TA TA TA TA TA TC TA TA TC 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
35123 CTA TA TA
1 -TA TA TA
35130 AGTCTAAACT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
1 1 0.03
2 37 0.93
3 2 0.05
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:35484 original size:27 final size:27
Alignment explanation
Indices: 35410--35490 Score: 117
Period size: 30 Copynumber: 2.9 Consensus size: 27
35400 TTTAGACTTA
35410 TTATTATTATTATAATAATTATTAAAC
1 TTATTATTATTATAATAATTATTAAAC
*
35437 TTATTATTAGTGGTATTATAATTATTAAAC
1 TTATTATTA-T--TATAATAATTATTAAAC
*
35467 TTATTATTATAATAATAATTATTA
1 TTATTATTATTATAATAATTATTA
35491 TTAGTGGTAT
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
27 21 0.44
28 1 0.02
29 1 0.02
30 25 0.52
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (27 bp):
TTATTATTATTATAATAATTATTAAAC
Done.