Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018345.1 Corchorus olitorius cultivar O-4 contig18378, 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: 52379
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.32
Found at i:1337 original size:37 final size:37
Alignment explanation
Indices: 1296--1370 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
1286 TAAATTTTAC
**
1296 TCCATCTCTAGGTAATTCATCAAAATAAAGCTAATAT
1 TCCATCTCTAGAAAATTCATCAAAATAAAGCTAATAT
1333 TCCATCTCTAGAAAATTCATCAAAATAAAGCTAATAT
1 TCCATCTCTAGAAAATTCATCAAAATAAAGCTAATAT
1370 T
1 T
1371 AATTGTTGCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.43, C:0.19, G:0.07, T:0.32
Consensus pattern (37 bp):
TCCATCTCTAGAAAATTCATCAAAATAAAGCTAATAT
Found at i:3151 original size:23 final size:23
Alignment explanation
Indices: 3125--3197 Score: 96
Period size: 23 Copynumber: 3.3 Consensus size: 23
3115 TATACTTAAC
3125 TTAAAATTACAACTTAAATAAAG
1 TTAAAATTACAACTTAAATAAAG
* *
3148 TTAAAA--GCAACTTAAATAAAT
1 TTAAAATTACAACTTAAATAAAG
*
3169 TTAAAATTACAACTTAAGTAAAG
1 TTAAAATTACAACTTAAATAAAG
*
3192 CTAAAA
1 TTAAAA
3198 ACAAAATAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
21 19 0.45
23 23 0.55
ACGTcount: A:0.56, C:0.10, G:0.05, T:0.29
Consensus pattern (23 bp):
TTAAAATTACAACTTAAATAAAG
Found at i:3160 original size:21 final size:22
Alignment explanation
Indices: 3125--3201 Score: 86
Period size: 21 Copynumber: 3.5 Consensus size: 22
3115 TATACTTAAC
3125 TTAAAATTACAACTTAAATAAAG
1 TTAAAA-TACAACTTAAATAAAG
* *
3148 TTAAAA-GCAACTTAAATAAAT
1 TTAAAATACAACTTAAATAAAG
*
3169 TTAAAATTACAACTTAAGTAAAG
1 TTAAAA-TACAACTTAAATAAAG
*
3192 CTAAAA-ACAA
1 TTAAAATACAA
3202 AATAAATTAG
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
21 23 0.50
23 23 0.50
ACGTcount: A:0.57, C:0.10, G:0.05, T:0.27
Consensus pattern (22 bp):
TTAAAATACAACTTAAATAAAG
Found at i:3208 original size:44 final size:44
Alignment explanation
Indices: 3125--3208 Score: 123
Period size: 44 Copynumber: 1.9 Consensus size: 44
3115 TATACTTAAC
* * **
3125 TTAAAATTACAACTTAAATAAAGTTAAAAGCAACTTAAATAAAT
1 TTAAAATTACAACTTAAATAAAGCTAAAAACAAAATAAATAAAT
*
3169 TTAAAATTACAACTTAAGTAAAGCTAAAAACAAAATAAAT
1 TTAAAATTACAACTTAAATAAAGCTAAAAACAAAATAAAT
3209 TAGACCATAG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 35 1.00
ACGTcount: A:0.58, C:0.10, G:0.05, T:0.27
Consensus pattern (44 bp):
TTAAAATTACAACTTAAATAAAGCTAAAAACAAAATAAATAAAT
Found at i:9179 original size:2 final size:2
Alignment explanation
Indices: 9172--9197 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
9162 AGAGTGGCTT
9172 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
9198 CAGGAGATAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:27811 original size:31 final size:29
Alignment explanation
Indices: 27766--27830 Score: 76
Period size: 31 Copynumber: 2.2 Consensus size: 29
27756 GTTTAATACC
* *
27766 CAAATTTGCTCCTTAACTATTCATTTTGGGA
1 CAAATTGGCCCCTTAACT-TT-ATTTTGGGA
* *
27797 TAAATTGGCCCCTTAACTTTTTTTTGGGA
1 CAAATTGGCCCCTTAACTTTATTTTGGGA
27826 CAAAT
1 CAAAT
27831 AAATCCCATA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
29 12 0.41
30 2 0.07
31 15 0.52
ACGTcount: A:0.26, C:0.18, G:0.14, T:0.42
Consensus pattern (29 bp):
CAAATTGGCCCCTTAACTTTATTTTGGGA
Found at i:29676 original size:211 final size:211
Alignment explanation
Indices: 29403--29825 Score: 846
Period size: 211 Copynumber: 2.0 Consensus size: 211
29393 TAATTCATCG
29403 TACCAGGAAAGCTAACTAGAATAAACGTAAATGTACAGCAAGAGCGACCTCTGACCAGAAACTAT
1 TACCAGGAAAGCTAACTAGAATAAACGTAAATGTACAGCAAGAGCGACCTCTGACCAGAAACTAT
29468 TTAATTTAGGATATTTGTCCATCGCCAAGTCTGAATTTGAAAATTAATACTTCAACCCATATTAT
66 TTAATTTAGGATATTTGTCCATCGCCAAGTCTGAATTTGAAAATTAATACTTCAACCCATATTAT
29533 CTACTATAAAGAAGAACCAATTCATCGTACTATCAAAGCTAACTAGAATAAACGTAAATGTACAG
131 CTACTATAAAGAAGAACCAATTCATCGTACTATCAAAGCTAACTAGAATAAACGTAAATGTACAG
29598 CAAAAGTGCCCTCTGA
196 CAAAAGTGCCCTCTGA
29614 TACCAGGAAAGCTAACTAGAATAAACGTAAATGTACAGCAAGAGCGACCTCTGACCAGAAACTAT
1 TACCAGGAAAGCTAACTAGAATAAACGTAAATGTACAGCAAGAGCGACCTCTGACCAGAAACTAT
29679 TTAATTTAGGATATTTGTCCATCGCCAAGTCTGAATTTGAAAATTAATACTTCAACCCATATTAT
66 TTAATTTAGGATATTTGTCCATCGCCAAGTCTGAATTTGAAAATTAATACTTCAACCCATATTAT
29744 CTACTATAAAGAAGAACCAATTCATCGTACTATCAAAGCTAACTAGAATAAACGTAAATGTACAG
131 CTACTATAAAGAAGAACCAATTCATCGTACTATCAAAGCTAACTAGAATAAACGTAAATGTACAG
29809 CAAAAGTGCCCTCTGA
196 CAAAAGTGCCCTCTGA
29825 T
1 T
29826 CAGAAACTAT
Statistics
Matches: 212, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
211 212 1.00
ACGTcount: A:0.40, C:0.20, G:0.14, T:0.26
Consensus pattern (211 bp):
TACCAGGAAAGCTAACTAGAATAAACGTAAATGTACAGCAAGAGCGACCTCTGACCAGAAACTAT
TTAATTTAGGATATTTGTCCATCGCCAAGTCTGAATTTGAAAATTAATACTTCAACCCATATTAT
CTACTATAAAGAAGAACCAATTCATCGTACTATCAAAGCTAACTAGAATAAACGTAAATGTACAG
CAAAAGTGCCCTCTGA
Found at i:29910 original size:157 final size:159
Alignment explanation
Indices: 29614--30017 Score: 587
Period size: 157 Copynumber: 2.5 Consensus size: 159
29604 TGCCCTCTGA
* * * *
29614 TACCAGGAAAGCTAACTAGAATAAACGTAAATGTACAGCAAGAGCGACCTCTGACCAGAAACTAT
1 TACCAGCAAAGCTAACTAGAATAAACGTAAATGTACAGCAAAAGTGACCTCTGATCAGAAACTAT
* * * * **
29679 TTAATTTAGGATATTTGTCCATCGCCAAGTCTGAATTTGAAAATTAATACTTCAACCCATATTAT
66 TTAATTTACGACATTAGTCCATCACCAAGTCTGAATCGGAAAATTAATACTTCAACCCATATTAT
*
29744 CTACTAT-AA-AGAAGAACCAATTCATCG
131 CTACAATAAAGAGAAGAACCAATTCATCG
* * *
29771 TACTATCAAAGCTAACTAGAATAAACGTAAATGTACAGCAAAAGTGCCCTCTGATCAGAAACTAT
1 TACCAGCAAAGCTAACTAGAATAAACGTAAATGTACAGCAAAAGTGACCTCTGATCAGAAACTAT
** *
29836 TTAATTTACGACATTAGTCCATCACCAAGTCTGGGTCGGGAAATTAATACTTCAACCCATATTAT
66 TTAATTTACGACATTAGTCCATCACCAAGTCTGAATCGGAAAATTAATACTTCAACCCATATTAT
*
29901 CTACAATAAAGTAGAAGAACTAATTCATCG
131 CTACAATAAAG-AGAAGAACCAATTCATCG
* * * *
29931 TACCAGCGAAGGTAACTAGAATGAACGTAAATGTACAGCAAAAATGACCTCTGATCAGAAACTAT
1 TACCAGCAAAGCTAACTAGAATAAACGTAAATGTACAGCAAAAGTGACCTCTGATCAGAAACTAT
29996 TTAATTTACGACATTAGTCCAT
66 TTAATTTACGACATTAGTCCAT
30018 TGCCGAGCTA
Statistics
Matches: 219, Mismatches: 25, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
157 120 0.55
158 2 0.01
160 97 0.44
ACGTcount: A:0.40, C:0.20, G:0.14, T:0.26
Consensus pattern (159 bp):
TACCAGCAAAGCTAACTAGAATAAACGTAAATGTACAGCAAAAGTGACCTCTGATCAGAAACTAT
TTAATTTACGACATTAGTCCATCACCAAGTCTGAATCGGAAAATTAATACTTCAACCCATATTAT
CTACAATAAAGAGAAGAACCAATTCATCG
Found at i:43095 original size:3 final size:3
Alignment explanation
Indices: 43087--43128 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
43077 GCAATAATTT
43087 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
43129 TTGATGAAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:44875 original size:2 final size:2
Alignment explanation
Indices: 44870--44897 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
44860 TCTTGAATGT
44870 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
44898 ATAATACTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:48084 original size:90 final size:91
Alignment explanation
Indices: 47900--48084 Score: 363
Period size: 90 Copynumber: 2.0 Consensus size: 91
47890 CATCATAGTA
47900 CTTTATTATGTTTTAGTTTTGACTTCACCAGAATTTCTTTTTCTTTTTTTTTCCCTCCTTTTGAA
1 CTTTATTATGTTTTAGTTTTGACTTCACCAGAATTTCTTTTTCTTTTTTTTTCCCTCCTTTTGAA
47965 GATCAACTAGGATCTAGTTGGCAATT
66 GATCAACTAGGATCTAGTTGGCAATT
47991 CTTTATTATGTTTTAGTTTTGACTTCACCAGAATTTCTTTTTC-TTTTTTTTCCCTCCTTTTGAA
1 CTTTATTATGTTTTAGTTTTGACTTCACCAGAATTTCTTTTTCTTTTTTTTTCCCTCCTTTTGAA
48055 GATCAACTAGGATCTAGTTGGCAATT
66 GATCAACTAGGATCTAGTTGGCAATT
48081 CTTT
1 CTTT
48085 TAAGGATAAT
Statistics
Matches: 94, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
90 51 0.54
91 43 0.46
ACGTcount: A:0.19, C:0.18, G:0.12, T:0.51
Consensus pattern (91 bp):
CTTTATTATGTTTTAGTTTTGACTTCACCAGAATTTCTTTTTCTTTTTTTTTCCCTCCTTTTGAA
GATCAACTAGGATCTAGTTGGCAATT
Found at i:51831 original size:15 final size:16
Alignment explanation
Indices: 51811--51840 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
51801 AGCACTTCTT
51811 TTGTTTTTTC-TTTTG
1 TTGTTTTTTCATTTTG
51826 TTGTTTTTTCATTTT
1 TTGTTTTTTCATTTT
51841 CCTCTTTGCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.03, C:0.07, G:0.10, T:0.80
Consensus pattern (16 bp):
TTGTTTTTTCATTTTG
Done.