Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023212.1 Corchorus olitorius cultivar O-4 contig23245, 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: 6224
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:790 original size:40 final size:39
Alignment explanation
Indices: 753--1618 Score: 989
Period size: 40 Copynumber: 21.7 Consensus size: 39
743 AGGATTAAAA
* *
753 TTGATAAAGCAATGATCCTGAGTAGGGTTTGAAATTAAT
1 TTGATAAAGCAATGATCCTGAGCAGGATTTGAAATTAAT
* *
792 TTGATAAA-AAGATGATCCTGAGCAGGATTCTGGAATTAAT
1 TTGATAAAGCA-ATGATCCTGAGCAGGATT-TGAAATTAAT
*
832 TTGGATAAAGCAATGATCCTGAGCAGGGTTTTGAAATTAAT
1 TT-GATAAAGCAATGATCCTGAGCA-GGATTTGAAATTAAT
* *
873 TTGATAAA-AAGATGATCGTGAGCAGGATTCTGAAATTAAT
1 TTGATAAAGCA-ATGATCCTGAGCAGGATT-TGAAATTAAT
* ** * *
913 TTGATAAAGAAATGATATTGTGCAGGGTTTTGAAATTAAT
1 TTGATAAAGCAATGATCCTGAGCA-GGATTTGAAATTAAT
* *
953 TTGATAAAGCAATGGTCTTGAGCAGGATTCTGAAATTAAT
1 TTGATAAAGCAATGATCCTGAGCAGGATT-TGAAATTAAT
* * *
993 TTGATAAA-AAGATGATCCTGTGCAGGATTCTGAAATCAAT
1 TTGATAAAGCA-ATGATCCTGAGCAGGATT-TGAAATTAAT
1033 TTGATAAAGCAATGATCCTGAGCAGGATTTTGAAATTAAT
1 TTGATAAAGCAATGATCCTGAGCAGGA-TTTGAAATTAAT
*
1073 TTGATAAA-AAGATGATCCTGAGCAGGATTTTGAAATTAAT
1 TTGATAAAGCA-ATGATCCTGAGCAGGA-TTTGAAATTAAT
* *
1113 TTGATAAAGCAATGATTCTGAGCAGGGTTTTGAAATTAAT
1 TTGATAAAGCAATGATCCTGAGCA-GGATTTGAAATTAAT
* * **
1153 TTGATAAAACAATGGTATTGAGCAGGATTCTGAAATTAAT
1 TTGATAAAGCAATGATCCTGAGCAGGATT-TGAAATTAAT
* * * *
1193 TTGATAAA-AAGATGATCATGTGCAGGATTCTGAAATCAAT
1 TTGATAAAGCA-ATGATCCTGAGCAGGATT-TGAAATTAAT
1233 TTGATAAAGCAATGATCCTGAGCAGGATTTTGAAATTAAT
1 TTGATAAAGCAATGATCCTGAGCAGGA-TTTGAAATTAAT
* *
1273 TTGATAAA-AAGATGATCCTGTGCAGGATTCTGAAATTAAT
1 TTGATAAAGCA-ATGATCCTGAGCAGGATT-TGAAATTAAT
* * *
1313 TTGATGAAGCGATGATCCTGAGCAGGGTTTTGAAATTAAT
1 TTGATAAAGCAATGATCCTGAGCA-GGATTTGAAATTAAT
* *
1353 TTGATAAA-AACATGATCCTGAGCAGGGTTTTGAAATTAAT
1 TTGATAAAGCA-ATGATCCTGAGCA-GGATTTGAAATTAAT
* * * *
1393 TTGGTAAAACAATGATCCTGAGCTGGATTCTGAAATTGAT
1 TTGATAAAGCAATGATCCTGAGCAGGATT-TGAAATTAAT
*
1433 TTGATAAA-AAGATGATCCTGAGCAGGATTCTGAAATTAAT
1 TTGATAAAGCA-ATGATCCTGAGCAGGATT-TGAAATTAAT
1473 TTGATAAAGCAATGATCCTGAGCAGGATTTTGAAATTAAT
1 TTGATAAAGCAATGATCCTGAGCAGGA-TTTGAAATTAAT
*
1513 TTGATAAAGCAATGATCTTGAGCAGGATTTTGAAATTAAT
1 TTGATAAAGCAATGATCCTGAGCAGGA-TTTGAAATTAAT
*
1553 TTGATAAAGCAATGACCCTGAGCAGGATTCTG--ATTAA-
1 TTGATAAAGCAATGATCCTGAGCAGGATT-TGAAATTAAT
* * *
1590 CTGGTAAAGAAATGATCCTGAGCAGGATT
1 TTGATAAAGCAATGATCCTGAGCAGGATT
1619 AAAACCCATA
Statistics
Matches: 723, Mismatches: 73, Indels: 64
0.84 0.08 0.07
Matches are distributed among these distances:
37 25 0.03
38 6 0.01
39 50 0.07
40 584 0.81
41 53 0.07
42 5 0.01
ACGTcount: A:0.37, C:0.10, G:0.22, T:0.32
Consensus pattern (39 bp):
TTGATAAAGCAATGATCCTGAGCAGGATTTGAAATTAAT
Found at i:1979 original size:137 final size:136
Alignment explanation
Indices: 1809--2208 Score: 619
Period size: 137 Copynumber: 2.9 Consensus size: 136
1799 ATGAAATGAA
1809 ATGAAATGATACCCGGAGGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATTGTGCCCGGAG
1 ATGAAATGATACCCGGAGGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATTGTGCCCGGAG
1874 GTCTTACAAATGCAAAACTCAACCTTGAGCAAGGTTTATTGAAATTTAAACGCAAATTTGATTAA
66 GTCTTACAAATGC-AAACTCAACCTTGAGCAAGGTTTATTGAAATTTAAACGCAAATTTGATTAA
1939 -AACCATG
130 CAA-CATG
*
1946 ATGAAATGATACCCAGAGGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATTGTGCCCGGAG
1 ATGAAATGATACCCGGAGGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATTGTGCCCGGAG
*
2011 GTC-TACAAATGCAAACTCGACCTTGAGCAAGGTTTATTGAAATTTAAACGCAAATTTGATTAAC
66 GTCTTACAAATGCAAACTCAACCTTGAGCAAGGTTTATTGAAATTTAAACGCAAATTTGATTAAC
*
2075 AATATG
131 AACATG
* *
2081 ATGAAATATGATGATACCCGGAGGATTTCATCAGAATTAATACCCGGAGGTTTCCGAAATCGTGC
1 ATG--A-A--ATGATACCCGGAGGATTT-ATCAGAATTAATACCCGGAGGTTTCTGAAATTGTGC
* * * *
2146 CCGGAGGTCTTACGAATGCAAACTCAACCTTGAGCAAGGTTT-TT-AAACTTAAACACAATTTTG
60 CCGGAGGTCTTACAAATGCAAACTCAACCTTGAGCAAGGTTTATTGAAATTTAAACGCAAATTTG
2209 CTGAAAAACT
Statistics
Matches: 244, Mismatches: 11, Indels: 13
0.91 0.04 0.05
Matches are distributed among these distances:
135 56 0.23
136 11 0.05
137 68 0.28
138 1 0.00
140 33 0.14
141 45 0.18
142 30 0.12
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (136 bp):
ATGAAATGATACCCGGAGGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATTGTGCCCGGAG
GTCTTACAAATGCAAACTCAACCTTGAGCAAGGTTTATTGAAATTTAAACGCAAATTTGATTAAC
AACATG
Found at i:3127 original size:11 final size:10
Alignment explanation
Indices: 3107--3142 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
3097 CTTTATTCCC
3107 TTTTTCTTTT
1 TTTTTCTTTT
*
3117 CTTTTCTTTT
1 TTTTTCTTTT
3127 TTCTTTCTTTT
1 TT-TTTCTTTT
3138 TTTTT
1 TTTTT
3143 GGCACTTGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
10 13 0.57
11 10 0.43
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:3127 original size:16 final size:16
Alignment explanation
Indices: 3107--3142 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
3097 CTTTATTCCC
3107 TTTTTCTTTTCTTTTCT
1 TTTTTC-TTTCTTTTCT
3124 TTTTTCTTTCTTTT-T
1 TTTTTCTTTCTTTTCT
3139 TTTT
1 TTTT
3143 GGCACTTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.26
16 8 0.42
17 6 0.32
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (16 bp):
TTTTTCTTTCTTTTCT
Found at i:3442 original size:7 final size:7
Alignment explanation
Indices: 3430--3456 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
3420 ATCTTATACT
3430 TTTTCAA
1 TTTTCAA
3437 TTTTCAA
1 TTTTCAA
3444 TTTTCAA
1 TTTTCAA
3451 TTTTCA
1 TTTTCA
3457 CTTTCACTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.26, C:0.15, G:0.00, T:0.59
Consensus pattern (7 bp):
TTTTCAA
Found at i:3502 original size:17 final size:16
Alignment explanation
Indices: 3480--3515 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
3470 TTTTTACTTC
*
3480 TTTTTTTCGTTTTCTTT
1 TTTTTTTCCTTTT-TTT
3497 TTTTTTTCCTTTTTTT
1 TTTTTTTCCTTTTTTT
3513 TTT
1 TTT
3516 GGCATATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.00, C:0.11, G:0.03, T:0.86
Consensus pattern (16 bp):
TTTTTTTCCTTTTTTT
Found at i:3950 original size:8 final size:8
Alignment explanation
Indices: 3933--3969 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
3923 TCCAAGTGCC
3933 TTTT-TCT
1 TTTTCTCT
3940 TTTTCTCT
1 TTTTCTCT
3948 TTTTCAT-T
1 TTTTC-TCT
3956 TTTTCTCT
1 TTTTCTCT
3964 TTTTCT
1 TTTTCT
3970 ATGAGAATTC
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
7 5 0.19
8 21 0.78
9 1 0.04
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTTCTCT
Done.