Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014049.1 Corchorus capsularis cultivar CVL-1 contig14070, 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: 52810
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:935 original size:15 final size:15
Alignment explanation
Indices: 915--944 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
905 AGTTTCATAT
915 GAAAGTCATAGATCA
1 GAAAGTCATAGATCA
*
930 GAAAGTCGTAGATCA
1 GAAAGTCATAGATCA
945 TACAATAATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.13, G:0.23, T:0.20
Consensus pattern (15 bp):
GAAAGTCATAGATCA
Found at i:2153 original size:20 final size:21
Alignment explanation
Indices: 2125--2166 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
2115 TCTTGGATTC
2125 TACTCTCACGGAA-TGTGAGT
1 TACTCTCACGGAATTGTGAGT
*
2145 TACTTTCACGGAATTGTGAGT
1 TACTCTCACGGAATTGTGAGT
2166 T
1 T
2167 TTCTTTGTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.36
Consensus pattern (21 bp):
TACTCTCACGGAATTGTGAGT
Found at i:3858 original size:16 final size:16
Alignment explanation
Indices: 3839--3870 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
3829 GGCTATCTCT
3839 CTGTTCTCTGTTTTCA
1 CTGTTCTCTGTTTTCA
3855 CTGTTCTCTGTTTTCA
1 CTGTTCTCTGTTTTCA
3871 TTTATTGTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.06, C:0.25, G:0.12, T:0.56
Consensus pattern (16 bp):
CTGTTCTCTGTTTTCA
Found at i:7732 original size:15 final size:16
Alignment explanation
Indices: 7709--7742 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
7699 TGTACGAGTC
7709 TAAGACTTAATTA-TT
1 TAAGACTTAATTACTT
*
7724 TAAGTCTTAATTACTT
1 TAAGACTTAATTACTT
7740 TAA
1 TAA
7743 TCAAACAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (16 bp):
TAAGACTTAATTACTT
Found at i:9024 original size:22 final size:22
Alignment explanation
Indices: 8975--9052 Score: 59
Period size: 22 Copynumber: 3.6 Consensus size: 22
8965 TTATGACCCC
* *
8975 ATTATGAAATTTTGATAATCTT
1 ATTATGAAATTTTAATAATCAT
** *
8997 CCTATGAAATTTTAATAATGAT
1 ATTATGAAATTTTAATAATCAT
* ** *
9019 ATTATGGAATTTCGATAATCTT
1 ATTATGAAATTTTAATAATCAT
*
9041 TTTAT-AAATTTT
1 ATTATGAAATTTT
9053 TTTTAACCTT
Statistics
Matches: 41, Mismatches: 15, Indels: 1
0.72 0.26 0.02
Matches are distributed among these distances:
21 5 0.12
22 36 0.88
ACGTcount: A:0.36, C:0.06, G:0.09, T:0.49
Consensus pattern (22 bp):
ATTATGAAATTTTAATAATCAT
Found at i:9075 original size:22 final size:22
Alignment explanation
Indices: 9042--9083 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
9032 GATAATCTTT
*
9042 TTATAAATTTTTTTTAACCTTC
1 TTATAAATTTTTGTTAACCTTC
9064 TTATGAAA-TTTTGTTAACCT
1 TTAT-AAATTTTTGTTAACCT
9084 CACTAAGGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.29, C:0.12, G:0.05, T:0.55
Consensus pattern (22 bp):
TTATAAATTTTTGTTAACCTTC
Found at i:9117 original size:22 final size:22
Alignment explanation
Indices: 9065--9119 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
9055 TTAACCTTCT
* *
9065 TATGAAATTTTGTTAACCTCAC
1 TATGAAATTTTGTAAACCTCAA
* *
9087 TAAGGAATTTTG-AAGACCTCAA
1 TATGAAATTTTGTAA-ACCTCAA
9109 TATGAAATTTT
1 TATGAAATTTT
9120 AATAACTTCC
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 1 0.04
22 25 0.96
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (22 bp):
TATGAAATTTTGTAAACCTCAA
Found at i:9188 original size:22 final size:23
Alignment explanation
Indices: 9140--9202 Score: 67
Period size: 22 Copynumber: 2.8 Consensus size: 23
9130 CAATGAAATT
*
9140 TTGATAACCAACACTATGAGATG
1 TTGATAACCAACACTATGAGATA
** *
9163 TTGATAACCTCCA-TATGATATA
1 TTGATAACCAACACTATGAGATA
*
9185 TTGATAACC-ACGCTATGA
1 TTGATAACCAACACTATGA
9203 AAATTTAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
21 1 0.03
22 21 0.64
23 11 0.33
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.30
Consensus pattern (23 bp):
TTGATAACCAACACTATGAGATA
Found at i:9258 original size:22 final size:22
Alignment explanation
Indices: 9233--9301 Score: 79
Period size: 22 Copynumber: 3.1 Consensus size: 22
9223 GAATTGTTAG
9233 TAATCACACTTTGAAATTTTGA
1 TAATCACACTTTGAAATTTTGA
* *
9255 TAATCACACTATGAAATTGTGA
1 TAATCACACTTTGAAATTTTGA
*
9277 TAA-C-CTCGTTATGAAATTTTGA
1 TAATCACAC-TT-TGAAATTTTGA
9299 TAA
1 TAA
9302 ATCTTCCTAT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
20 2 0.05
21 2 0.05
22 36 0.90
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.38
Consensus pattern (22 bp):
TAATCACACTTTGAAATTTTGA
Found at i:9293 original size:44 final size:43
Alignment explanation
Indices: 8974--9543 Score: 272
Period size: 44 Copynumber: 13.0 Consensus size: 43
8964 ATTATGACCC
* **
8974 CATTATGAAATTTTGATAATCTTCCTATGAAATTTTAATAATGAT
1 CATTATGAAATTTTGATAATC-TCCTATGAAATTTTGATAA-CCT
* * ** **
9019 -ATTATGGAATTTCGATAATCTTTTTAT-AAATTTTTTTTAACCTT
1 CATTATGAAATTTTGATAATC-TCCTATGAAA-TTTTGATAACC-T
* * * *
9063 C-TTATGAAATTTTGTTAACCTCACTAAGGAATTTTGA-AGACCT
1 CATTATGAAATTTTGATAATCTC-CTATGAAATTTTGATA-ACCT
* * * *
9106 CAATATGAAATTTTAATAA-CTTCCCAATGAAATTTTGATAACCAA
1 CATTATGAAATTTTGATAATC-T-CCTATGAAATTTTGATAACC-T
* * * * * * *
9151 CACTATGAGATGTTGATAACCTCCATATGATATATTGATAACCA
1 CATTATGAAATTTTGATAATCTCC-TATGAAATTTTGATAACCT
** * * * * * * *
9195 CGCTATGAAAATTTAAAAACCTCCATACG-AATTGTT-AGTAATCA
1 CATTATGAAATTTTGATAATCTCC-TATGAAATT-TTGA-TAACCT
* *
9239 CACTT-TGAAATTTTGATAATCACACTATGAAATTGTGATAACCT
1 CA-TTATGAAATTTTGATAATCTC-CTATGAAATTTTGATAACCT
* *
9283 CGTTATGAAATTTTGATAAATCTTCCTATAAAATTTTGATAAACCT
1 CATTATGAAATTTTGAT-AATC-TCCTATGAAATTTTGAT-AACCT
* * * * * *
9329 CCTTATAAAATTTTGATAACTTTCTTATGAAATCTTGATAAACT
1 CATTATGAAATTTTGATAA-TCTCCTATGAAATTTTGATAACCT
* **
9373 -A--A--AAATTTTGATAAGCTCCCTATGATTTTTTGATAACCT
1 CATTATGAAATTTTGATAATCT-CCTATGAAATTTTGATAACCT
* * *
9412 CATTATGAAATTTTGTTAATCTCTCTATGAAATTTTGATCTACAT
1 CATTATGAAATTTTGATAATCTC-CTATGAAATTTTGAT-AACCT
* * *
9457 -ATTATGAAATTTTGATAACCCTCTTATGAAATTTTGA-AAACT
1 CATTATGAAATTTTGATAA-TCTCCTATGAAATTTTGATAACCT
* * * * * *
9499 AAACTATG-AATTTTGATAACCTTCATATAAAATTTTGATATCCT
1 -CATTATGAAATTTTGATAATC-TCCTATGAAATTTTGATAACCT
9543 C
1 C
9544 CTTGAAATTT
Statistics
Matches: 398, Mismatches: 90, Indels: 76
0.71 0.16 0.13
Matches are distributed among these distances:
38 1 0.00
39 28 0.07
40 1 0.00
41 1 0.00
42 5 0.01
43 39 0.10
44 219 0.55
45 81 0.20
46 23 0.06
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.40
Consensus pattern (43 bp):
CATTATGAAATTTTGATAATCTCCTATGAAATTTTGATAACCT
Found at i:9318 original size:23 final size:23
Alignment explanation
Indices: 9290--9370 Score: 94
Period size: 23 Copynumber: 3.6 Consensus size: 23
9280 CCTCGTTATG
9290 AAATTTTGATAAATCTTCCTATA
1 AAATTTTGATAAATCTTCCTATA
*
9313 AAATTTTGATAAA-CCTCCTTATA
1 AAATTTTGATAAATCTTCC-TATA
* * *
9336 AAATTTTGATAACT-TTCTTATG
1 AAATTTTGATAAATCTTCCTATA
*
9358 AAATCTTGATAAA
1 AAATTTTGATAAA
9371 CTAAAAATTT
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
22 18 0.37
23 31 0.63
ACGTcount: A:0.40, C:0.12, G:0.06, T:0.42
Consensus pattern (23 bp):
AAATTTTGATAAATCTTCCTATA
Found at i:9361 original size:22 final size:21
Alignment explanation
Indices: 9264--9538 Score: 159
Period size: 22 Copynumber: 12.7 Consensus size: 21
9254 ATAATCACAC
* *
9264 TATGAAATTGTGATAACCTCGT
1 TATGAAATTTTGATAACTTC-T
*
9286 TATGAAATTTTGATAAATCTTCC
1 TATGAAATTTTGAT-AA-CTTCT
* *
9309 TATAAAATTTTGATAAACCTCCT
1 TATGAAATTTTGAT-AA-CTTCT
*
9332 TATAAAATTTTGATAACTTTCT
1 TATGAAATTTTGATAAC-TTCT
* *
9354 TATGAAATCTTGATAA--AC-
1 TATGAAATTTTGATAACTTCT
* * *
9372 TA-AAAATTTTGATAAGCTCCC
1 TATGAAATTTTGATAA-CTTCT
** *
9393 TATGATTTTTTGATAACCTCAT
1 TATGAAATTTTGATAACTTC-T
*
9415 TATGAAATTTTGTTAA-TCTCT
1 TATGAAATTTTGATAACT-TCT
* * *
9436 CTATGAAATTTTGATCTACATAT
1 -TATGAAATTTTGAT-AACTTCT
*
9459 TATGAAATTTTGATAACCCTCT
1 TATGAAATTTTGATAA-CTTCT
* *
9481 TATGAAATTTTGAAAACTAAAC-
1 TATGAAATTTTGATAACT--TCT
*
9503 TATG-AATTTTGATAACCTTCA
1 TATGAAATTTTGATAA-CTTCT
*
9524 TATAAAATTTTGATA
1 TATGAAATTTTGATA
9539 TCCTCCTTGA
Statistics
Matches: 197, Mismatches: 37, Indels: 38
0.72 0.14 0.14
Matches are distributed among these distances:
17 11 0.06
18 2 0.01
19 1 0.01
20 2 0.01
21 21 0.11
22 118 0.60
23 39 0.20
24 3 0.02
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.42
Consensus pattern (21 bp):
TATGAAATTTTGATAACTTCT
Found at i:9368 original size:45 final size:45
Alignment explanation
Indices: 9246--9371 Score: 134
Period size: 45 Copynumber: 2.8 Consensus size: 45
9236 TCACACTTTG
* * *
9246 AAATTTTGAT-AATC-ACACTATGAAATTGTGAT-AACCTCGTTATG
1 AAATTTTGATAAATCTTC-CTATGAAATT-TGATAAACCTCCTTATA
*
9290 AAATTTTGATAAATCTTCCTATAAAATTTTGATAAACCTCCTTATA
1 AAATTTTGATAAATCTTCCTATGAAA-TTTGATAAACCTCCTTATA
* *
9336 AAATTTTGATAACT-TTCTTATGAAATCTTGATAAAC
1 AAATTTTGATAAATCTTCCTATGAAAT-TTGATAAAC
9372 TAAAAATTTT
Statistics
Matches: 70, Mismatches: 7, Indels: 9
0.81 0.08 0.10
Matches are distributed among these distances:
44 11 0.16
45 33 0.47
46 26 0.37
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.40
Consensus pattern (45 bp):
AAATTTTGATAAATCTTCCTATGAAATTTGATAAACCTCCTTATA
Found at i:9734 original size:22 final size:22
Alignment explanation
Indices: 9663--10051 Score: 81
Period size: 22 Copynumber: 17.6 Consensus size: 22
9653 AATCACATTT
* * * *
9663 TGAAAATTTGAAAACCTCTTTA
1 TGAAATTTTGATAACCCCTCTA
* *
9685 TGAAATTTTGATAACCTCTTTA
1 TGAAATTTTGATAACCCCTCTA
* * *
9707 TAAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAACCCCTCTA
* * *
9729 TGAAATTCTGATAATCACAT-TA
1 TGAAATTTTGATAA-CCCCTCTA
* * *
9751 TGTAATTTTCAT--CTCGCT-T-
1 TGAAATTTTGATAAC-CCCTCTA
* * ** *
9770 TGAGATTTTGCTAACAACACTA
1 TGAAATTTTGATAACCCCTCTA
* *
9792 TGAAATTTTGATAA-TCTTCATA
1 TGAAATTTTGATAACCCCTC-TA
*
9814 T-AAATTTTGATAATCCGATCTCTA
1 TGAAATTTTGATAA-CC--CCTCTA
* * *
9838 TGAAATTTCGATAATCACTCTA
1 TGAAATTTTGATAACCCCTCTA
* * * *
9860 TTAGA-TTTGATAA-TCTTCTA
1 TGAAATTTTGATAACCCCTCTA
* ** *
9880 TCAAATTTTG-GCACTCCT-TA
1 TGAAATTTTGATAACCCCTCTA
* *
9900 TGAAATTGAGACTTTTATAA-CCTTCATA
1 TGAAA-T-----TTTGATAACCCCTC-TA
* *
9928 TGAAATTTTGATAACCACACTA
1 TGAAATTTTGATAACCCCTCTA
* *
9950 TAAAATTTTGATAACCTCC-CCA
1 TGAAATTTTGATAACC-CCTCTA
* *
9972 TGAAATATT-AGTAACCTCCT-AA
1 TGAAATTTTGA-TAACC-CCTCTA
* * *
9994 TGAAATTTTGTTAACCACACTA
1 TGAAATTTTGATAACCCCTCTA
* *
10016 TGAAATTCTT-ATAACCTCGCTA
1 TGAAATT-TTGATAACCCCTCTA
*
10038 TGACATTTTGATAA
1 TGAAATTTTGATAA
10052 TCTCTTTGGT
Statistics
Matches: 262, Mismatches: 74, Indels: 62
0.66 0.19 0.16
Matches are distributed among these distances:
19 9 0.03
20 17 0.06
21 34 0.13
22 163 0.62
23 8 0.03
24 4 0.02
25 13 0.05
26 5 0.02
27 2 0.01
28 7 0.03
ACGTcount: A:0.34, C:0.17, G:0.10, T:0.39
Consensus pattern (22 bp):
TGAAATTTTGATAACCCCTCTA
Found at i:9889 original size:21 final size:22
Alignment explanation
Indices: 9789--9889 Score: 93
Period size: 21 Copynumber: 4.6 Consensus size: 22
9779 GCTAACAACA
9789 CTATGAAATTTTGATAATC-TT
1 CTATGAAATTTTGATAATCATT
9810 CATAT-AAATTTTGATAATCCGATCT
1 C-TATGAAATTTTGATAAT-C-AT-T
* *
9835 CTATGAAATTTCGATAATCACT
1 CTATGAAATTTTGATAATCATT
* *
9857 CTATTAGA-TTTGATAATC-TT
1 CTATGAAATTTTGATAATCATT
*
9877 CTATCAAATTTTG
1 CTATGAAATTTTG
9890 GCACTCCTTA
Statistics
Matches: 65, Mismatches: 8, Indels: 14
0.75 0.09 0.16
Matches are distributed among these distances:
20 7 0.11
21 27 0.42
22 11 0.17
23 1 0.02
24 5 0.08
25 14 0.22
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.44
Consensus pattern (22 bp):
CTATGAAATTTTGATAATCATT
Found at i:9975 original size:44 final size:42
Alignment explanation
Indices: 9927--10051 Score: 124
Period size: 44 Copynumber: 2.8 Consensus size: 42
9917 TAACCTTCAT
* * * *
9927 ATGAAATTTTGATAACCACACTATAAAATTTTGATAACCTCCCC
1 ATGAAATTTT-ATAACCTC-CTATGAAATTTTGATAACCACACC
* * *
9971 ATGAAATATTAGTAACCTCCTAATGAAATTTTGTTAACCACACT
1 ATGAAATTTTA-TAACCTCCT-ATGAAATTTTGATAACCACACC
*
10015 ATGAAATTCTTATAACCTCGCTATGACATTTTGATAA
1 ATGAAATT-TTATAACCTC-CTATGAAATTTTGATAA
10052 TCTCTTTGGT
Statistics
Matches: 67, Mismatches: 10, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
43 3 0.04
44 59 0.88
45 5 0.07
ACGTcount: A:0.38, C:0.19, G:0.09, T:0.34
Consensus pattern (42 bp):
ATGAAATTTTATAACCTCCTATGAAATTTTGATAACCACACC
Found at i:14150 original size:37 final size:37
Alignment explanation
Indices: 14087--14174 Score: 115
Period size: 37 Copynumber: 2.4 Consensus size: 37
14077 TCCAAATAGG
* *
14087 ACGTTGGAGACCAAGACAAAAAGCAAAATTAAATACA
1 ACGTTGGAAACAAAGACAAAAAGCAAAATTAAATACA
* **
14124 ACGATTGGAAACAAAGAC-AAAGGCAAAATTAAATAGG
1 ACG-TTGGAAACAAAGACAAAAAGCAAAATTAAATACA
14161 ACGTTGGAAACAAA
1 ACGTTGGAAACAAA
14175 AAATCAAATT
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
36 11 0.24
37 22 0.49
38 12 0.27
ACGTcount: A:0.53, C:0.14, G:0.19, T:0.14
Consensus pattern (37 bp):
ACGTTGGAAACAAAGACAAAAAGCAAAATTAAATACA
Found at i:14329 original size:32 final size:33
Alignment explanation
Indices: 14293--14360 Score: 97
Period size: 31 Copynumber: 2.1 Consensus size: 33
14283 TTAATAATGG
14293 CAATTTAGAAATATGTTTT--AAAATAAAGGGTA
1 CAATTTAGAAATATGTTTTAGAAAAT-AAGGGTA
*
14325 CAA-TTGGAAATATGTTTTAGAAAATAAGGGTA
1 CAATTTAGAAATATGTTTTAGAAAATAAGGGTA
14357 CAAT
1 CAAT
14361 CGGAAAATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
31 14 0.44
32 13 0.41
33 5 0.16
ACGTcount: A:0.46, C:0.04, G:0.18, T:0.32
Consensus pattern (33 bp):
CAATTTAGAAATATGTTTTAGAAAATAAGGGTA
Found at i:14335 original size:31 final size:32
Alignment explanation
Indices: 14300--14366 Score: 102
Period size: 32 Copynumber: 2.1 Consensus size: 32
14290 TGGCAATTTA
*
14300 GAAATATGTTTT--AAAATAAAGGGTACAATTG
1 GAAATATGTTTTAGAAAAT-AAGGGTACAATCG
14331 GAAATATGTTTTAGAAAATAAGGGTACAATCG
1 GAAATATGTTTTAGAAAATAAGGGTACAATCG
14363 GAAA
1 GAAA
14367 ATATAAAGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
31 12 0.36
32 16 0.48
33 5 0.15
ACGTcount: A:0.46, C:0.04, G:0.21, T:0.28
Consensus pattern (32 bp):
GAAATATGTTTTAGAAAATAAGGGTACAATCG
Found at i:15240 original size:38 final size:38
Alignment explanation
Indices: 15189--15264 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
15179 AGGACTCTCG
15189 TTCGGTCTCTATGAGCATTCTCGCTCGGTCTCTACAAA
1 TTCGGTCTCTATGAGCATTCTCGCTCGGTCTCTACAAA
*
15227 TTCGGTCTCTATGAGCATTCTTGCTCGGTCTCTACAAA
1 TTCGGTCTCTATGAGCATTCTCGCTCGGTCTCTACAAA
15265 CTAACAATCA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.18, C:0.28, G:0.18, T:0.36
Consensus pattern (38 bp):
TTCGGTCTCTATGAGCATTCTCGCTCGGTCTCTACAAA
Found at i:18009 original size:26 final size:26
Alignment explanation
Indices: 17973--18024 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
17963 TGTCATACTT
17973 AGTTTAGACCAATAATATTATAACAA
1 AGTTTAGACCAATAATATTATAACAA
17999 AGTTTAGACCAATAATATTATAACAA
1 AGTTTAGACCAATAATATTATAACAA
18025 GTCAAAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.50, C:0.12, G:0.08, T:0.31
Consensus pattern (26 bp):
AGTTTAGACCAATAATATTATAACAA
Found at i:19815 original size:47 final size:47
Alignment explanation
Indices: 19761--19857 Score: 194
Period size: 47 Copynumber: 2.1 Consensus size: 47
19751 AATTACACGT
19761 TAGGGAAATAATAAATTTTAATCATAATAATACATTAAACTATCAAA
1 TAGGGAAATAATAAATTTTAATCATAATAATACATTAAACTATCAAA
19808 TAGGGAAATAATAAATTTTAATCATAATAATACATTAAACTATCAAA
1 TAGGGAAATAATAAATTTTAATCATAATAATACATTAAACTATCAAA
19855 TAG
1 TAG
19858 AACATGTCAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 50 1.00
ACGTcount: A:0.53, C:0.08, G:0.07, T:0.32
Consensus pattern (47 bp):
TAGGGAAATAATAAATTTTAATCATAATAATACATTAAACTATCAAA
Found at i:20898 original size:1 final size:1
Alignment explanation
Indices: 20894--20919 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
20884 CCTTTTTGAC
20894 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
20920 GCTTTACTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:26179 original size:37 final size:37
Alignment explanation
Indices: 26129--26207 Score: 140
Period size: 37 Copynumber: 2.1 Consensus size: 37
26119 ATTGGTTTAA
*
26129 TAGAAAAGATCCTTTTTTTGGAAAATTATATCCTAAC
1 TAGAAAACATCCTTTTTTTGGAAAATTATATCCTAAC
*
26166 TAGAAAACATCCTTTTTTTGGAAAATTATATTCTAAC
1 TAGAAAACATCCTTTTTTTGGAAAATTATATCCTAAC
26203 TAGAA
1 TAGAA
26208 TACCACCTAG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.38
Consensus pattern (37 bp):
TAGAAAACATCCTTTTTTTGGAAAATTATATCCTAAC
Found at i:28993 original size:15 final size:15
Alignment explanation
Indices: 28973--29003 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
28963 CAGAATCATG
28973 ATGATGACCACCACC
1 ATGATGACCACCACC
*
28988 ATGATGACCTCCACC
1 ATGATGACCACCACC
29003 A
1 A
29004 CCACCTGTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.39, G:0.13, T:0.16
Consensus pattern (15 bp):
ATGATGACCACCACC
Found at i:29151 original size:21 final size:21
Alignment explanation
Indices: 29125--29164 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
29115 TTATGATGAT
*
29125 CTCCGGCATCAGAGTTGGCGG
1 CTCCGGCATCAGAATTGGCGG
29146 CTCCGGCATCAGAATTGGC
1 CTCCGGCATCAGAATTGGC
29165 AGCGGCAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.30, G:0.33, T:0.20
Consensus pattern (21 bp):
CTCCGGCATCAGAATTGGCGG
Found at i:37058 original size:13 final size:12
Alignment explanation
Indices: 37032--37069 Score: 53
Period size: 11 Copynumber: 3.2 Consensus size: 12
37022 AAAATCAAAC
37032 AAAATGA-AAGA
1 AAAATGAGAAGA
37043 AAAATGAGAGAGA
1 AAAATGAGA-AGA
37056 AAAA-GAGAAGA
1 AAAATGAGAAGA
37067 AAA
1 AAA
37070 TTGGAATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 13 0.52
12 5 0.20
13 7 0.28
ACGTcount: A:0.71, C:0.00, G:0.24, T:0.05
Consensus pattern (12 bp):
AAAATGAGAAGA
Found at i:39316 original size:106 final size:106
Alignment explanation
Indices: 39131--39344 Score: 394
Period size: 106 Copynumber: 2.0 Consensus size: 106
39121 AAAATCTAAA
39131 ATCTAAATCTAAAACACATATAATGATAACCCCCTTTCACAATGGGGTTACAAGCGTTTTAATTG
1 ATCTAAATCTAAAACACATATAATGATAACCCCCTTTCACAATGGGGTTACAAGCGTTTTAATTG
39196 GGGGGTGACACTTGTCCCCTC-AATGGCCACCTAAATGGGTT
66 GGGGGTGACACTTGTCCCC-CAAATGGCCACCTAAATGGGTT
*
39237 ATCTAAATCTAAAACACATATAATGATAACCCCCTTTCACAATGGGGTTACAAGTGTTTTAATTG
1 ATCTAAATCTAAAACACATATAATGATAACCCCCTTTCACAATGGGGTTACAAGCGTTTTAATTG
*
39302 GGGGGTGGCACTTGTCCCCCAAATGGCCACCTAAATGGGTT
66 GGGGGTGACACTTGTCCCCCAAATGGCCACCTAAATGGGTT
39343 AT
1 AT
39345 TAATGCAATA
Statistics
Matches: 105, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
105 1 0.01
106 104 0.99
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (106 bp):
ATCTAAATCTAAAACACATATAATGATAACCCCCTTTCACAATGGGGTTACAAGCGTTTTAATTG
GGGGGTGACACTTGTCCCCCAAATGGCCACCTAAATGGGTT
Found at i:40263 original size:26 final size:27
Alignment explanation
Indices: 40234--40288 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
40224 AAAATATATA
**
40234 TTAATTGCTTG-TTTAATCCATATACC
1 TTAATTGCTTGAGGTAATCCATATACC
**
40260 TTAATTTTTTGAGGTAATCCATATACC
1 TTAATTGCTTGAGGTAATCCATATACC
40287 TT
1 TT
40289 CATTAGCTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 9 0.38
27 15 0.62
ACGTcount: A:0.27, C:0.16, G:0.09, T:0.47
Consensus pattern (27 bp):
TTAATTGCTTGAGGTAATCCATATACC
Found at i:46372 original size:14 final size:14
Alignment explanation
Indices: 46353--46386 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
46343 GTGATTAAGC
*
46353 CCTTCCAGTTCCTT
1 CCTTCCACTTCCTT
*
46367 CCTTCCCCTTCCTT
1 CCTTCCACTTCCTT
46381 CCTTCC
1 CCTTCC
46387 CCTCTAAGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.03, C:0.53, G:0.03, T:0.41
Consensus pattern (14 bp):
CCTTCCACTTCCTT
Found at i:46387 original size:14 final size:14
Alignment explanation
Indices: 46361--46389 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
46351 GCCCTTCCAG
46361 TTCCTTCCTTCCCC
1 TTCCTTCCTTCCCC
46375 TTCCTTCCTTCCCC
1 TTCCTTCCTTCCCC
46389 T
1 T
46390 CTAAGTTGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.55, G:0.00, T:0.45
Consensus pattern (14 bp):
TTCCTTCCTTCCCC
Found at i:52728 original size:2 final size:2
Alignment explanation
Indices: 52721--52807 Score: 165
Period size: 2 Copynumber: 43.0 Consensus size: 2
52711 AAGAAGAAGA
52721 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
52763 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG ATG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A-G AG
52806 AG
1 AG
52808 TAG
Statistics
Matches: 84, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
2 82 0.98
3 2 0.02
ACGTcount: A:0.49, C:0.00, G:0.49, T:0.01
Consensus pattern (2 bp):
AG
Done.