Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014422.1 Corchorus olitorius cultivar O-4 contig14455, 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: 5848
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:148 original size:26 final size:28
Alignment explanation
Indices: 115--173 Score: 77
Period size: 30 Copynumber: 2.1 Consensus size: 28
105 ATCCAATATT
115 TTATTTTTT-A-AAATTATGAAAAGATA
1 TTATTTTTTGAGAAATTATGAAAAGATA
*
141 TTATTTTTTGAGGTTAATTATGAAAAGATA
1 TTATTTTTTGA-G-AAATTATGAAAAGATA
171 TTA
1 TTA
174 ATAATCTACT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 9 0.32
27 1 0.04
30 18 0.64
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (28 bp):
TTATTTTTTGAGAAATTATGAAAAGATA
Found at i:2861 original size:2 final size:2
Alignment explanation
Indices: 2856--2904 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
2846 TATATATATA
2856 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
2898 TG TG TG T
1 TG TG TG T
2905 AATTTACCCT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:3691 original size:94 final size:94
Alignment explanation
Indices: 3515--3691 Score: 225
Period size: 94 Copynumber: 1.9 Consensus size: 94
3505 TTTCCTAAAA
*
3515 AGGTTAACAAAATTTCATAGGGAGGTTATGAAAATTTTATGGAGAGGTTATCAAAATTATATAGA
1 AGGTTAACAAAATTTCATAGGGAGGTTATCAAAATTTTATGGAGAGGTTATCAAAATTATATAGA
***
3580 GAAGATATCACGGTTTCATTCTCATAGGG
66 GAAGATATCAAAATTTCATTCTCATAGGG
* * * *
3609 AGGTTATCTAAATTTCAT-GGTGTGGTTATCAAAATTTTAT-GAGGAGGTTATCAAAATTTTATA
1 AGGTTAACAAAATTTCATAGG-GAGGTTATCAAAATTTTATGGA-GAGGTTATCAAAATTATATA
*
3672 G-GGAGATTATCAAAATTTCA
64 GAGAAGA-TATCAAAATTTCA
3692 CAATGAGGTT
Statistics
Matches: 71, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
93 8 0.11
94 63 0.89
ACGTcount: A:0.36, C:0.08, G:0.21, T:0.35
Consensus pattern (94 bp):
AGGTTAACAAAATTTCATAGGGAGGTTATCAAAATTTTATGGAGAGGTTATCAAAATTATATAGA
GAAGATATCAAAATTTCATTCTCATAGGG
Found at i:3723 original size:22 final size:22
Alignment explanation
Indices: 3319--3796 Score: 229
Period size: 22 Copynumber: 21.5 Consensus size: 22
3309 TTACATGAGA
**
3319 AGGTTATCAAAATTTCATACAG
1 AGGTTATCAAAATTTCATAGTG
* ***
3341 AGGTTACCAAAATTTCATAAAA
1 AGGTTATCAAAATTTCATAGTG
* *
3363 AGGTTATCAAAATTTCTTAGGG
1 AGGTTATCAAAATTTCATAGTG
* * ***
3385 AGGTTAACAAAATATCATACAA
1 AGGTTATCAAAATTTCATAGTG
*
3407 AGGTTATCAAAATTTTATAGTG
1 AGGTTATCAAAATTTCATAGTG
* *
3429 TA-GTTATCAAAATTTAATAAG-A
1 -AGGTTATCAAAATTTCAT-AGTG
* *
3451 AGGTTAACAAAATTTCATAGGGAGG
1 AGGTTATCAAAATTTCATA--G-TG
3476 AAGGTTATCAAAA-TT--T-GT-
1 -AGGTTATCAAAATTTCATAGTG
* * * ***
3494 -GCTTATTAAAATTTCCTAAAA
1 AGGTTATCAAAATTTCATAGTG
* *
3515 AGGTTAACAAAATTTCATAGGG
1 AGGTTATCAAAATTTCATAGTG
* * * *
3537 AGGTTATGAAAATTTTATGGAG
1 AGGTTATCAAAATTTCATAGTG
*
3559 AGGTTATCAAAATTAT-ATAGAG
1 AGGTTATCAAAATT-TCATAGTG
* * ** *
3581 AAGATATCACGGTTTCATTCTCATAGGG
1 AGGTTATCA-----AAATT-TCATAGTG
* *
3609 AGGTTATCTAAATTTCATGGTG
1 AGGTTATCAAAATTTCATAGTG
* *
3631 TGGTTATCAAAATTTTATGAG-G
1 AGGTTATCAAAATTTCAT-AGTG
* *
3653 AGGTTATCAAAATTTTATAGGG
1 AGGTTATCAAAATTTCATAGTG
* * *
3675 AGATTATCAAAATTTCACAATG
1 AGGTTATCAAAATTTCATAGTG
3697 AGGTTATCAAAATTTCATAGTG
1 AGGTTATCAAAATTTCATAGTG
* * * **
3719 TGGTTATTAAGATTTCACCGTG
1 AGGTTATCAAAATTTCATAGTG
* * * *
3741 TGGTTATCAAATTTTCACAGGG
1 AGGTTATCAAAATTTCATAGTG
** * *
3763 AGGTTATCGACCATTTCATAATA
1 AGGTTATC-AAAATTTCATAGTG
3786 AGGTTATCAAA
1 AGGTTATCAAA
3797 TGTTCACAGT
Statistics
Matches: 341, Mismatches: 91, Indels: 48
0.71 0.19 0.10
Matches are distributed among these distances:
16 9 0.03
17 2 0.01
19 1 0.00
20 1 0.00
21 4 0.01
22 271 0.79
23 25 0.07
25 2 0.01
26 11 0.03
27 4 0.01
28 11 0.03
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.34
Consensus pattern (22 bp):
AGGTTATCAAAATTTCATAGTG
Found at i:3734 original size:44 final size:44
Alignment explanation
Indices: 3608--3824 Score: 166
Period size: 44 Copynumber: 4.9 Consensus size: 44
3598 TTCTCATAGG
* * * ** *
3608 GAGGTTATCTAAATTTCATGGTGTGGTTATCAAAATTTTATGAG
1 GAGGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCACAAT
* * * *
3652 GAGGTTATCAAAATTTTATAGGGAGATTATCAAAATTTCACAAT
1 GAGGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCACAAT
* * **
3696 GAGGTTATCAAAATTTCATAGTGTGGTTATTAAGATTTCACCGT
1 GAGGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCACAAT
* * * * * ** *
3740 GTGGTTATCAAATTTTCACAGGGAGGTTATCGACCATTTCATAAT
1 GAGGTTATCAAAATTTCATAGTGTGGTTATC-AAAATTTCACAAT
* * * * *
3785 AAGGTTATC-AAATGTTCACAGTATTGTTATCAATATTTCA
1 GAGGTTATCAAAAT-TTCATAGTGTGGTTATCAAAATTTCA
3825 ACGTTGGAGC
Statistics
Matches: 133, Mismatches: 38, Indels: 4
0.76 0.22 0.02
Matches are distributed among these distances:
44 105 0.79
45 28 0.21
ACGTcount: A:0.33, C:0.11, G:0.18, T:0.38
Consensus pattern (44 bp):
GAGGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCACAAT
Found at i:3814 original size:89 final size:88
Alignment explanation
Indices: 3654--3824 Score: 202
Period size: 89 Copynumber: 1.9 Consensus size: 88
3644 TTTATGAGGA
* * * *
3654 GGTTATCAAAATTTTATAGGGAGATTATCAAAATTTCACAATGAGGTTATCAAAATTTCATAGTG
1 GGTTATCAAAATTTTACAGGGAGATTATCAAAATTTCACAATAAGGTTATCAAAATTTCACAGTA
*
3719 TGGTTATTAAGATTTCACCGTGT
66 TGGTTATCAAGATTTCACCGTGT
* ** *
3742 GGTTATC-AAATTTTCACAGGGAGGTTATCGACCATTTCATAATAAGGTTATC-AAATGTTCACA
1 GGTTATCAAAATTTT-ACAGGGAGATTATC-AAAATTTCACAATAAGGTTATCAAAAT-TTCACA
* *
3805 GTATTGTTATCAATATTTCA
63 GTATGGTTATCAAGATTTCA
3825 ACGTTGGAGC
Statistics
Matches: 69, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
87 7 0.10
88 23 0.33
89 39 0.57
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.37
Consensus pattern (88 bp):
GGTTATCAAAATTTTACAGGGAGATTATCAAAATTTCACAATAAGGTTATCAAAATTTCACAGTA
TGGTTATCAAGATTTCACCGTGT
Found at i:4807 original size:48 final size:48
Alignment explanation
Indices: 4710--4807 Score: 169
Period size: 48 Copynumber: 2.0 Consensus size: 48
4700 ATGAATGGTC
** *
4710 TTAAATTTGTTAATACATATATAACTTTTTTCATAATCGTTGTAGCTT
1 TTAAATTTGTTAATACATATATAACTTTTTTCATAATCGTTACAACTT
4758 TTAAATTTGTTAATACATATATAACTTTTTTCATAATCGTTACAACTT
1 TTAAATTTGTTAATACATATATAACTTTTTTCATAATCGTTACAACTT
4806 TT
1 TT
4808 TCAGTAACTA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.33, C:0.11, G:0.06, T:0.50
Consensus pattern (48 bp):
TTAAATTTGTTAATACATATATAACTTTTTTCATAATCGTTACAACTT
Done.