Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009740.1 Corchorus capsularis cultivar CVL-1 contig09761, 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: 9043
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.34
Found at i:10 original size:2 final size:2
Alignment explanation
Indices: 4--40 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1 TCT
4 TA TA 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 TA TA T
41 TAAGAGCTCC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1240 original size:89 final size:88
Alignment explanation
Indices: 1123--1311 Score: 342
Period size: 89 Copynumber: 2.1 Consensus size: 88
1113 CCTAAGATTC
1123 ATGTCTGATCCAACCTAATTTGTTTATTTTCCTAGTGCACAGATTATGCTTCTCCCGTCAGTACA
1 ATGT-TGAT-CAACCTAATTTGTTTATTTTCCTAGTGCACAGATTATGCTTCTCCCGTCAGTACA
1188 TCACACAATCCCTAAAACAATCTAT
64 TCACACAATCCCTAAAACAATCTAT
*
1213 ATGTTGATCAACCTAATTTTTTTTATTTTCCTAGTGCACAGATTATGCTTCTCCCGTCAGTACAT
1 ATGTTGATCAACCTAA-TTTGTTTATTTTCCTAGTGCACAGATTATGCTTCTCCCGTCAGTACAT
1278 CACACAATCCCTAAAACAATCTAT
65 CACACAATCCCTAAAACAATCTAT
1302 ATGTTGATCA
1 ATGTTGATCA
1312 GACATATAAA
Statistics
Matches: 97, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
88 8 0.08
89 85 0.88
90 4 0.04
ACGTcount: A:0.29, C:0.25, G:0.10, T:0.36
Consensus pattern (88 bp):
ATGTTGATCAACCTAATTTGTTTATTTTCCTAGTGCACAGATTATGCTTCTCCCGTCAGTACATC
ACACAATCCCTAAAACAATCTAT
Found at i:2782 original size:3 final size:3
Alignment explanation
Indices: 2774--2798 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2764 ATATATATAT
2774 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
2799 CAATTAATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:2880 original size:2 final size:2
Alignment explanation
Indices: 2873--2905 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2863 TGTCCACCAA
2873 AT AT 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 AT AT A
2906 CACACTATAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4132 original size:23 final size:23
Alignment explanation
Indices: 4082--4188 Score: 128
Period size: 23 Copynumber: 4.7 Consensus size: 23
4072 AAATTTGTAG
* * *
4082 TTATCAAGATTTCATAAGAAAG-
1 TTATCAAAATTTCATAGGAAGGT
* *
4104 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTCATAGGAAGGT
* *
4127 TTATCAAAATTTTATAGGAAGAT
1 TTATCAAAATTTCATAGGAAGGT
*
4150 TTATCAAAATTTCATAGCAAGG-
1 TTATCAAAATTTCATAGGAAGGT
4172 TTATCAAAATTTCATAG
1 TTATCAAAATTTCATAG
4189 TGTGATTATC
Statistics
Matches: 74, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
22 34 0.46
23 40 0.54
ACGTcount: A:0.41, C:0.08, G:0.14, T:0.36
Consensus pattern (23 bp):
TTATCAAAATTTCATAGGAAGGT
Found at i:4176 original size:45 final size:44
Alignment explanation
Indices: 4016--4207 Score: 157
Period size: 45 Copynumber: 4.5 Consensus size: 44
4006 GTCAATAAAG
* * * * **
4016 GGAAGATTAACAAAATTTCATAACGAGGTTATAAAAAAATCATA
1 GGAAGATTATCAAAATTTCATAGCAAGGTTATCAAAATTTCATA
* * *
4060 GGGAGATTATCAAAA-TT--T-G-TA-GTTATCAAGATTTCATA
1 GGAAGATTATCAAAATTTCATAGCAAGGTTATCAAAATTTCATA
* * ** *
4098 AGAA-AGTTATCAAAATTTTATAGGGAGGTTTATCAAAATTTTATA
1 GGAAGA-TTATCAAAATTTCATAGCAAGG-TTATCAAAATTTCATA
4143 GGAAGATTTATCAAAATTTCATAGCAAGGTTATCAAAATTTCATA
1 GGAAGA-TTATCAAAATTTCATAGCAAGGTTATCAAAATTTCATA
*
4188 GTG-TGATTATCAAAATTTCA
1 G-GAAGATTATCAAAATTTCA
4208 GAGTATGATT
Statistics
Matches: 118, Mismatches: 20, Indels: 20
0.75 0.13 0.13
Matches are distributed among these distances:
37 1 0.01
38 24 0.20
39 3 0.03
41 2 0.02
42 1 0.01
43 3 0.03
44 28 0.24
45 35 0.30
46 21 0.18
ACGTcount: A:0.43, C:0.08, G:0.15, T:0.34
Consensus pattern (44 bp):
GGAAGATTATCAAAATTTCATAGCAAGGTTATCAAAATTTCATA
Found at i:4188 original size:22 final size:22
Alignment explanation
Indices: 4081--4207 Score: 130
Period size: 22 Copynumber: 5.7 Consensus size: 22
4071 AAAATTTGTA
* * *
4081 GTTATCAAGATTTCATAAGAAA
1 GTTATCAAAATTTCATAGGAAG
* *
4103 GTTATCAAAATTTTATAGGGAG
1 GTTATCAAAATTTCATAGGAAG
*
4125 GTTTATCAAAATTTTATAGGAAG
1 G-TTATCAAAATTTCATAGGAAG
* *
4148 ATTTATCAAAATTTCATAGCAAG
1 -GTTATCAAAATTTCATAGGAAG
*
4171 GTTATCAAAATTTCATAGTG-TG
1 GTTATCAAAATTTCATAG-GAAG
*
4193 ATTATCAAAATTTCA
1 GTTATCAAAATTTCA
4208 GAGTATGATT
Statistics
Matches: 89, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
22 50 0.56
23 39 0.44
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.37
Consensus pattern (22 bp):
GTTATCAAAATTTCATAGGAAG
Found at i:4274 original size:22 final size:22
Alignment explanation
Indices: 4249--4291 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
4239 TTTTAAATTT
*
4249 TCATAACGTGGTTATCAATATA
1 TCATAACGAGGTTATCAATATA
**
4271 TCATATGGAGGTTATCAATAT
1 TCATAACGAGGTTATCAATAT
4292 CGAGGTTTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (22 bp):
TCATAACGAGGTTATCAATATA
Found at i:4376 original size:22 final size:22
Alignment explanation
Indices: 4349--4411 Score: 92
Period size: 22 Copynumber: 2.9 Consensus size: 22
4339 TCCCATTATG
4349 AAATTTCATAGTGATG-TTATCA
1 AAATTTCATAGTG-TGATTATCA
*
4371 CAATTTCATAGTGTGATTATCA
1 AAATTTCATAGTGTGATTATCA
*
4393 AAATTTCAGAGTGTGATTA
1 AAATTTCATAGTGTGATTA
4412 CTAACAATTC
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
21 2 0.05
22 35 0.95
ACGTcount: A:0.35, C:0.10, G:0.16, T:0.40
Consensus pattern (22 bp):
AAATTTCATAGTGTGATTATCA
Found at i:4626 original size:22 final size:22
Alignment explanation
Indices: 4601--4708 Score: 71
Period size: 22 Copynumber: 4.9 Consensus size: 22
4591 TTCCTTAGGG
4601 AGGTTAATAAAATTTCATAAGA
1 AGGTTAATAAAATTTCATAAGA
* *
4623 AGGTTAAAAAAAATTT-ATAAAA
1 AGGTT-AATAAAATTTCATAAGA
* *
4645 AGGTT-CTCGAAATTTCAT-AGTA
1 AGGTTAAT-AAAATTTCATAAG-A
*** * *
4667 TCATTATTAAAATTTCATAGGA
1 AGGTTAATAAAATTTCATAAGA
4689 AGGTT-ATCAAAATTTCATAA
1 AGGTTAAT-AAAATTTCATAA
4709 TGGGATCATA
Statistics
Matches: 62, Mismatches: 17, Indels: 14
0.67 0.18 0.15
Matches are distributed among these distances:
21 8 0.13
22 43 0.69
23 11 0.18
ACGTcount: A:0.46, C:0.07, G:0.12, T:0.34
Consensus pattern (22 bp):
AGGTTAATAAAATTTCATAAGA
Found at i:5425 original size:45 final size:45
Alignment explanation
Indices: 5302--5427 Score: 116
Period size: 45 Copynumber: 2.8 Consensus size: 45
5292 AATCACACTC
* * *
5302 TAAAATTTTGAT-AATC-ACACTATGAAATTGTGAT-AATCTCGCTA
1 TAAAATTTTGATAAATCTTC-CTATGAAATT-TGATAAACCTCCCTA
* *
5346 TGAAATTTTGATAAATCTTCCTATAAAATTTTGATAAACCTCCCTA
1 TAAAATTTTGATAAATCTTCCTATGAAA-TTTGATAAACCTCCCTA
* * *
5392 TAAAATTTTGTTAACT-TTCTTATGAAATCTTGATAA
1 TAAAATTTTGATAAATCTTCCTATGAAAT-TTGATAA
5428 CTACAAATTT
Statistics
Matches: 67, Mismatches: 10, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
44 12 0.18
45 31 0.46
46 24 0.36
ACGTcount: A:0.37, C:0.13, G:0.09, T:0.40
Consensus pattern (45 bp):
TAAAATTTTGATAAATCTTCCTATGAAATTTGATAAACCTCCCTA
Found at i:5633 original size:22 final size:22
Alignment explanation
Indices: 5114--5633 Score: 220
Period size: 22 Copynumber: 23.8 Consensus size: 22
5104 AAATTTTTTT
* * * *
5114 TAACCTTCTTATGAAATTTGGT
1 TAACCTCCCTATGAAATTTTGA
* *
5136 TAACCTCCCTAAGGAATTTT-A
1 TAACCTCCCTATGAAATTTTGA
* * **
5157 AAGAGCTCAATATGAAATTTTGA
1 TA-ACCTCCCTATGAAATTTTGA
* *
5180 TAACTTCCCAATGAAATTTTGA
1 TAACCTCCCTATGAAATTTTGA
* * * *
5202 TAACCAACACTATGAGATATTGA
1 TAACC-TCCCTATGAAATTTTGA
* * * * *
5225 TAACCTCCATATCATATATTGG
1 TAACCTCCCTATGAAATTTTGA
** * *
5247 TAA-CTACGTTATGAAAATTTAA
1 TAACCT-CCCTATGAAATTTTGA
* * *
5269 AAATCTCCGTATG-AATTGTT-A
1 TAACCTCCCTATGAAATT-TTGA
* * * * *
5290 GTAATCACACTCTAAAATTTTGA
1 -TAACCTCCCTATGAAATTTTGA
* * * *
5313 TAATCACACTATGAAATTGTGA
1 TAACCTCCCTATGAAATTTTGA
* *
5335 TAATCTCGCTATGAAATTTTGA
1 TAACCTCCCTATGAAATTTTGA
* * *
5357 TAAATCTTCCTATAAAATTTTGA
1 T-AACCTCCCTATGAAATTTTGA
* *
5380 TAAACCTCCCTATAAAATTTTGT
1 T-AACCTCCCTATGAAATTTTGA
* * * *
5403 TAACTTTCTTATGAAATCTTGA
1 TAACCTCCCTATGAAATTTTGA
*
5425 TAA-----CTA-CAAATTTTGA
1 TAACCTCCCTATGAAATTTTGA
**
5441 TAACCTCCCTATGATTTTTTGA
1 TAACCTCCCTATGAAATTTTGA
** ** *
5463 TAACCTCATTATGAGTTTTTGT
1 TAACCTCCCTATGAAATTTTGA
*
5485 TAATCTCCCTATGAAATTTTGA
1 TAACCTCCCTATGAAATTTTGA
* * *
5507 TCTACAT-ACTATGAAATTTTGA
1 T-AACCTCCCTATGAAATTTTGA
* *
5529 TAACC-CTCTTGTGAAATTTTGA
1 TAACCTC-CCTATGAAATTTTGA
* **
5551 -AAACTAAACTATGAAATTTTGA
1 TAACCT-CCCTATGAAATTTTGA
* *
5573 TAACCTTCATATGAAATTTTGA
1 TAACCTCCCTATGAAATTTTGA
* * *
5595 TAACCACACTATAAAATTTTGA
1 TAACCTCCCTATGAAATTTTGA
*
5617 TAACCTCCCCATGAAAT
1 TAACCTCCCTATGAAAT
5634 ATTTAATGAA
Statistics
Matches: 367, Mismatches: 109, Indels: 44
0.71 0.21 0.08
Matches are distributed among these distances:
16 11 0.03
17 2 0.01
21 15 0.04
22 268 0.73
23 71 0.19
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (22 bp):
TAACCTCCCTATGAAATTTTGA
Found at i:5765 original size:22 final size:22
Alignment explanation
Indices: 5740--6004 Score: 139
Period size: 22 Copynumber: 12.0 Consensus size: 22
5730 AATTAACTAC
*
5740 CCTATGAAATTTCAATAACCAA
1 CCTATGAAATTTTAATAACCAA
* * *
5762 CCTAAGAGATTTTAATAACCTGAT
1 CCTATGAAATTTTAATAACC--AA
**
5786 CCTATGAAATTTTGGTAACCATA
1 CCTATGAAATTTTAATAACCA-A
**
5809 -CTATGAAATTTTGGTAACC-A
1 CCTATGAAATTTTAATAACCAA
* ** *
5829 CACTATGGAATTTTGGTAACC-T
1 C-CTATGAAATTTTAATAACCAA
* *
5851 CCTCATGAAATTATAATAACCAT
1 CCT-ATGAAATTTTAATAACCAA
* **
5874 CTTATGAAATTTTGGTAACCATA
1 CCTATGAAATTTTAATAACCA-A
**
5897 -CTATGAAATTTTGGTAACC-A
1 CCTATGAAATTTTAATAACCAA
* **
5917 CACTATGGAATTTTGGTAACCATA
1 C-CTATGAAATTTTAATAACCA-A
** *
5941 -CTATGAAATTTTGGTAACC-T
1 CCTATGAAATTTTAATAACCAA
* *
5961 CCTTATGAAATTATAATAACCAT
1 CC-TATGAAATTTTAATAACCAA
* *
5984 CTTATGAAATTTTGATAACCA
1 CCTATGAAATTTTAATAACCA
6005 TATAGAGACA
Statistics
Matches: 198, Mismatches: 30, Indels: 30
0.77 0.12 0.12
Matches are distributed among these distances:
20 2 0.01
21 3 0.02
22 170 0.86
23 5 0.03
24 18 0.09
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.35
Consensus pattern (22 bp):
CCTATGAAATTTTAATAACCAA
Found at i:5898 original size:88 final size:88
Alignment explanation
Indices: 5774--6004 Score: 315
Period size: 88 Copynumber: 2.6 Consensus size: 88
5764 TAAGAGATTT
*
5774 TAATAACCTGATCCTATGAAATTTTGGTAACCATACTATGAAATTTTGGTAACCACACTATGGAA
1 TAATAACC--ATCTTATGAAATTTTGGTAACCATACTATGAAATTTTGGTAACCACACTATGGAA
*
5839 TTTTGGTAACC-TCCTCATGAAATTA
64 TTTTGGTAACCATACT-ATGAAATTA
5864 TAATAACCATCTTATGAAATTTTGGTAACCATACTATGAAATTTTGGTAACCACACTATGGAATT
1 TAATAACCATCTTATGAAATTTTGGTAACCATACTATGAAATTTTGGTAACCACACTATGGAATT
*
5929 TTGGTAACCATACTATGAAATTT
66 TTGGTAACCATACTATGAAATTA
** * ** *
5952 TGGTAACC-TCCTTATGAAATTATAATAACCAT-CTTATGAAATTTTGATAACCA
1 TAATAACCAT-CTTATGAAATTTTGGTAACCATAC-TATGAAATTTTGGTAACCA
6005 TATAGAGACA
Statistics
Matches: 129, Mismatches: 9, Indels: 8
0.88 0.06 0.05
Matches are distributed among these distances:
87 2 0.02
88 116 0.90
89 3 0.02
90 8 0.06
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.35
Consensus pattern (88 bp):
TAATAACCATCTTATGAAATTTTGGTAACCATACTATGAAATTTTGGTAACCACACTATGGAATT
TTGGTAACCATACTATGAAATTA
Found at i:6005 original size:22 final size:22
Alignment explanation
Indices: 5784--6005 Score: 254
Period size: 22 Copynumber: 10.1 Consensus size: 22
5774 TAATAACCTG
5784 ATCCTATGAAATTTTGGTAACC
1 ATCCTATGAAATTTTGGTAACC
*
5806 ATACTATGAAATTTTGGTAACC
1 ATCCTATGAAATTTTGGTAACC
*
5828 A-CACTATGGAATTTTGGTAACC
1 ATC-CTATGAAATTTTGGTAACC
* **
5850 -TCCTCATGAAATTATAATAACC
1 ATCCT-ATGAAATTTTGGTAACC
*
5872 ATCTTATGAAATTTTGGTAACC
1 ATCCTATGAAATTTTGGTAACC
*
5894 ATACTATGAAATTTTGGTAACC
1 ATCCTATGAAATTTTGGTAACC
*
5916 A-CACTATGGAATTTTGGTAACC
1 ATC-CTATGAAATTTTGGTAACC
*
5938 ATACTATGAAATTTTGGTAACC
1 ATCCTATGAAATTTTGGTAACC
* **
5960 -TCCTTATGAAATTATAATAACC
1 ATCC-TATGAAATTTTGGTAACC
* *
5982 ATCTTATGAAATTTTGATAACC
1 ATCCTATGAAATTTTGGTAACC
6004 AT
1 AT
6006 ATAGAGACAA
Statistics
Matches: 168, Mismatches: 24, Indels: 16
0.81 0.12 0.08
Matches are distributed among these distances:
21 4 0.02
22 159 0.95
23 5 0.03
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.36
Consensus pattern (22 bp):
ATCCTATGAAATTTTGGTAACC
Found at i:6194 original size:19 final size:19
Alignment explanation
Indices: 6170--6206 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
6160 TATTGACATT
6170 TAAAAT-TTGAAATTAAAAG
1 TAAAATATT-AAATTAAAAG
6189 TAAAATATTAAATTAAAA
1 TAAAATATTAAATTAAAA
6207 AAATAATAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.32
Consensus pattern (19 bp):
TAAAATATTAAATTAAAAG
Found at i:6395 original size:38 final size:35
Alignment explanation
Indices: 6337--6413 Score: 109
Period size: 38 Copynumber: 2.1 Consensus size: 35
6327 AATTTAAGAC
6337 CAAAGACAAAACAAAATTAAATACAACGATTGGAAA
1 CAAAGACAAAACAAAATTAAATACAACG-TTGGAAA
**
6373 CAAAGACAAAAGACAAAATTAAATAGGACGTTGGAAA
1 CAAAGAC-AAA-ACAAAATTAAATACAACGTTGGAAA
6410 CAAA
1 CAAA
6414 AAGTCAAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
36 7 0.19
37 14 0.38
38 16 0.43
ACGTcount: A:0.60, C:0.13, G:0.14, T:0.13
Consensus pattern (35 bp):
CAAAGACAAAACAAAATTAAATACAACGTTGGAAA
Found at i:6614 original size:2 final size:2
Alignment explanation
Indices: 6607--6651 Score: 54
Period size: 2 Copynumber: 21.5 Consensus size: 2
6597 TTCGTACTTT
* *
6607 TA TA TA TA GTA TA GA TA TA TA TA TA TA TA TA TA TA CA CTA TA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
6651 T
1 T
6652 TATTTTTGTC
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
2 34 0.92
3 3 0.08
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.44
Consensus pattern (2 bp):
TA
Found at i:6637 original size:23 final size:23
Alignment explanation
Indices: 6607--6651 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
6597 TTCGTACTTT
*
6607 TATATATAGTATAGA-TATATATA
1 TATATATA-TATACACTATATATA
6630 TATATATATATACACTATATAT
1 TATATATATATACACTATATAT
6652 TATTTTTGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.44
Consensus pattern (23 bp):
TATATATATATACACTATATATA
Found at i:6808 original size:11 final size:11
Alignment explanation
Indices: 6792--6823 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
6782 TACTATATAT
6792 CTAATTAATAG
1 CTAATTAATAG
*
6803 CTAATTAATAT
1 CTAATTAATAG
6814 CTAATTAATA
1 CTAATTAATA
6824 ATGAATAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.47, C:0.09, G:0.03, T:0.41
Consensus pattern (11 bp):
CTAATTAATAG
Found at i:7154 original size:11 final size:11
Alignment explanation
Indices: 7138--7180 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
7128 TATACTATAT
7138 CTAATTAATAG
1 CTAATTAATAG
*
7149 CTAATTAATAT
1 CTAATTAATAG
7160 CTAATTAATAG
1 CTAATTAATAG
*
7171 TTAATTAATA
1 CTAATTAATA
7181 ATGAATAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.42
Consensus pattern (11 bp):
CTAATTAATAG
Found at i:7162 original size:22 final size:22
Alignment explanation
Indices: 7134--7180 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
7124 CCATTATACT
7134 ATATCTAATTAATAGCTAATTA
1 ATATCTAATTAATAGCTAATTA
*
7156 ATATCTAATTAATAGTTAATTA
1 ATATCTAATTAATAGCTAATTA
7178 ATA
1 ATA
7181 ATGAATAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (22 bp):
ATATCTAATTAATAGCTAATTA
Found at i:7283 original size:357 final size:350
Alignment explanation
Indices: 6635--7345 Score: 1230
Period size: 357 Copynumber: 2.0 Consensus size: 350
6625 ATATATATAT
6635 ATATATACACTATATATTATTTTTGTCCCCTATGGAAATTACTAACAAGCCCTTTCAACTTTTAA
1 ATATATACACTATATATTATTTTTGTCCCCTATGGAAATTACTAACAAGCCCTTTCAACTTTTAA
* *
6700 CTTGGTGCCACCTTATCGCCCCATTTTGGTAATTTCTCACATCTAACATATTAATTTAAAGCCCC
66 CCTGGTGCCACCTTATCGCCCCATTTTGGTAATTTATCACATCTAACATATTAATTTAAAGCCCC
6765 TCCTTAACCATCCATTATACTATATATCTAATTAATAGCTAATTAATATCTAATTAATAATGAAT
131 TCCTTAACCATCCATTATACTATATATCTAATTAATAGCTAATTAATATCTAATTAATAATGAAT
6830 AAATTCAATATGATTAAAAGGGAATAATAGCTAATTAATACCTAATTATTCCCCTTCATCCCCAT
196 AAATTCAATATGATTAAAAGGGAATAATAGCTAATTAATACCTAATTATTCCCCTTCATCCCCAT
*
6895 TTTTTTGATTACATAAGAAGATT-AAAAAAAAATGATTAAAAGGGAATTATGCTTCTCAATATTC
261 TTTTTTGATTACACAAGAAGATTAAAAAAAAAATGATTAAAAGGGAATTATGCTTCTCAATATTC
*
6959 AAGCCTACTGATGACATTAGCCTAC
326 AAGCCCACTGATGACATTAGCCTAC
*
6984 ATATATATACTATATATTATTTTTGTCCCCTATGGAAATTACTAACAAGCCCTTTCAACTTTTAA
1 ATATATACACTATATATTATTTTTGTCCCCTATGGAAATTACTAACAAGCCCTTTCAACTTTTAA
7049 CCTGGTGCCACCTTATCG-CCCATTTTGGTAATTTATCACATCTAACATATTAATTTAAAGCCCC
66 CCTGGTGCCACCTTATCGCCCCATTTTGGTAATTTATCACATCTAACATATTAATTTAAAGCCCC
*
7113 TCCTTAACCATCCATTATACTATATCTAATTAATAGCTAATTAATATCTAATTAATAGT-TAATT
131 TCCTTAACCATCCATTATAC--TA--T-A-T-AT--CTAATTAATAGCTAATTAATA-TCTAATT
7177 AATAATGAATAAATTCAATATGATTAAAAGGGAATAATAGCTAATTAATACCTAATTATTCCCCT
186 AATAATGAATAAATTCAATATGATTAAAAGGGAATAATAGCTAATTAATACCTAATTATTCCCCT
* *
7242 TCTTCCTCATTTTTTTGATTACACAAGAAGATTAGAAAAAAAAATGATTAAAAGGGAATTATGCT
251 TCATCCCCATTTTTTTGATTACACAAGAAGATTA-AAAAAAAAATGATTAAAAGGGAATTATGCT
7307 TCTCAATATTCAAGCCCACTGATGACATTAGCCTAC
315 TCTCAATATTCAAGCCCACTGATGACATTAGCCTAC
7343 ATA
1 ATA
7346 CCTATTATTC
Statistics
Matches: 342, Mismatches: 8, Indels: 14
0.94 0.02 0.04
Matches are distributed among these distances:
348 65 0.19
349 81 0.24
350 2 0.01
352 1 0.00
353 1 0.00
354 1 0.00
355 2 0.01
357 120 0.35
358 1 0.00
359 68 0.20
ACGTcount: A:0.37, C:0.19, G:0.09, T:0.36
Consensus pattern (350 bp):
ATATATACACTATATATTATTTTTGTCCCCTATGGAAATTACTAACAAGCCCTTTCAACTTTTAA
CCTGGTGCCACCTTATCGCCCCATTTTGGTAATTTATCACATCTAACATATTAATTTAAAGCCCC
TCCTTAACCATCCATTATACTATATATCTAATTAATAGCTAATTAATATCTAATTAATAATGAAT
AAATTCAATATGATTAAAAGGGAATAATAGCTAATTAATACCTAATTATTCCCCTTCATCCCCAT
TTTTTTGATTACACAAGAAGATTAAAAAAAAAATGATTAAAAGGGAATTATGCTTCTCAATATTC
AAGCCCACTGATGACATTAGCCTAC
Done.