Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007559.1 Corchorus capsularis cultivar CVL-1 contig07580, 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: 13472
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.30
Found at i:10701 original size:7 final size:7
Alignment explanation
Indices: 10681--10761 Score: 74
Period size: 7 Copynumber: 11.4 Consensus size: 7
10671 AAAAAGAAAC
10681 AAAAAGT
1 AAAAAGT
10688 AAAAAGT
1 AAAAAGT
10695 AAAAAGT
1 AAAAAGT
*
10702 AAAGAGT
1 AAAAAGT
**
10709 AATCAGT
1 AAAAAGT
*
10716 AAAGAGT
1 AAAAAGT
*
10723 AAAATGGT
1 AAAA-AGT
10731 AAAAAGT
1 AAAAAGT
*
10738 AAAGAGT
1 AAAAAGT
*
10745 AATCAA-T
1 AA-AAAGT
10752 AAAAAGT
1 AAAAAGT
10759 AAA
1 AAA
10762 GTGGTAAAGA
Statistics
Matches: 59, Mismatches: 12, Indels: 6
0.77 0.16 0.08
Matches are distributed among these distances:
6 2 0.03
7 50 0.85
8 7 0.12
ACGTcount: A:0.63, C:0.02, G:0.17, T:0.17
Consensus pattern (7 bp):
AAAAAGT
Found at i:10775 original size:7 final size:7
Alignment explanation
Indices: 10685--10776 Score: 60
Period size: 7 Copynumber: 12.9 Consensus size: 7
10675 AGAAACAAAA
*
10685 AGTAAAA
1 AGTAAAG
*
10692 AGTAAAA
1 AGTAAAG
10699 AGTAAAG
1 AGTAAAG
**
10706 AGTAATC
1 AGTAAAG
10713 AGTAAAG
1 AGTAAAG
10720 AGTAAA-
1 AGTAAAG
*
10726 ATGGTAAAA
1 A--GTAAAG
10735 AGTAAAG
1 AGTAAAG
**
10742 AGTAATC
1 AGTAAAG
* *
10749 AATAAAA
1 AGTAAAG
10756 AGTAAAG
1 AGTAAAG
*
10763 TGGTAAAG
1 -AGTAAAG
10771 AGTAAA
1 AGTAAA
10777 TGGTAATTAG
Statistics
Matches: 66, Mismatches: 15, Indels: 8
0.74 0.17 0.09
Matches are distributed among these distances:
6 1 0.02
7 53 0.80
8 11 0.17
9 1 0.02
ACGTcount: A:0.59, C:0.02, G:0.21, T:0.18
Consensus pattern (7 bp):
AGTAAAG
Found at i:10783 original size:36 final size:36
Alignment explanation
Indices: 10681--10776 Score: 140
Period size: 36 Copynumber: 2.7 Consensus size: 36
10671 AAAAAGAAAC
* *
10681 AAAAAGTAAAA-AGTAAAAAGTAAAGAGTAATCAGT
1 AAAAAGTAAAATGGTAAAAAGTAAAGAGTAATCAAT
*
10716 AAAGAGTAAAATGGTAAAAAGTAAAGAGTAATCAAT
1 AAAAAGTAAAATGGTAAAAAGTAAAGAGTAATCAAT
* *
10752 AAAAAGTAAAGTGGTAAAGAGTAAA
1 AAAAAGTAAAATGGTAAAAAGTAAA
10777 TGGTAATTAG
Statistics
Matches: 54, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
35 10 0.19
36 44 0.81
ACGTcount: A:0.60, C:0.02, G:0.20, T:0.18
Consensus pattern (36 bp):
AAAAAGTAAAATGGTAAAAAGTAAAGAGTAATCAAT
Found at i:10792 original size:36 final size:36
Alignment explanation
Indices: 10681--10792 Score: 131
Period size: 36 Copynumber: 3.1 Consensus size: 36
10671 AAAAAGAAAC
* *
10681 AAAAAGTAAAA-AGTAAAAAGTAAAGAGTAATCAGT
1 AAAAAGTAAAATGGTAAAAAGTAAAGAGTAATCAGA
*
10716 AAAGAGTAAAATGGTAAAAAGTAAAGAGTAATCA-A
1 AAAAAGTAAAATGGTAAAAAGTAAAGAGTAATCAGA
* * *
10751 TAAAAAGTAAAGTGGTAAAGAGTAAATG-GTAATTAGA
1 -AAAAAGTAAAATGGTAAAAAGTAAA-GAGTAATCAGA
10788 AAAAA
1 AAAAA
10793 AGATTAAAAA
Statistics
Matches: 66, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
35 10 0.15
36 54 0.82
37 2 0.03
ACGTcount: A:0.60, C:0.02, G:0.20, T:0.19
Consensus pattern (36 bp):
AAAAAGTAAAATGGTAAAAAGTAAAGAGTAATCAGA
Found at i:10828 original size:28 final size:28
Alignment explanation
Indices: 10789--10874 Score: 115
Period size: 25 Copynumber: 3.1 Consensus size: 28
10779 GTAATTAGAA
*
10789 AAAAAGATTAAAAATGGTATTCAATAGT
1 AAAAAGAGTAAAAATGGTATTCAATAGT
10817 AAAAAGAGTAAAAATGGTATTC---AGT
1 AAAAAGAGTAAAAATGGTATTCAATAGT
* *
10842 AAAAAGAGTAAAAATGGTAATTAAATGGT
1 AAAAAGAGTAAAAATGGT-ATTCAATAGT
10871 AAAA
1 AAAA
10875 GGTAAATAGT
Statistics
Matches: 51, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
25 21 0.41
26 3 0.06
28 21 0.41
29 6 0.12
ACGTcount: A:0.56, C:0.02, G:0.17, T:0.24
Consensus pattern (28 bp):
AAAAAGAGTAAAAATGGTATTCAATAGT
Found at i:10846 original size:54 final size:52
Alignment explanation
Indices: 10767--10903 Score: 151
Period size: 53 Copynumber: 2.7 Consensus size: 52
10757 GTAAAGTGGT
* *
10767 AAAGAGTAAATGGTAATTAGAAAAAAAGATTAAAAATGGT-ATTCAATAGTAA
1 AAAGAGTAAATGGTAATTAG-AAAAAAGAGTAAAAATGGTAATTAAATAGTAA
* *
10819 AAAGAGTAAAAATGGT-ATTCAGTAAAAAGAGTAAAAATGGTAATTAAATGGT-A
1 AAAGAGT--AAATGGTAATT-AGAAAAAAGAGTAAAAATGGTAATTAAATAGTAA
*
10872 AAAG-GTAAATAGTAATTAG--AAAAGAGTAAAAA
1 AAAGAGTAAATGGTAATTAGAAAAAAGAGTAAAAA
10904 ATAGTAAAAA
Statistics
Matches: 75, Mismatches: 5, Indels: 14
0.80 0.05 0.15
Matches are distributed among these distances:
48 13 0.17
50 8 0.11
51 3 0.04
52 9 0.12
53 25 0.33
54 17 0.23
ACGTcount: A:0.56, C:0.01, G:0.19, T:0.23
Consensus pattern (52 bp):
AAAGAGTAAATGGTAATTAGAAAAAAGAGTAAAAATGGTAATTAAATAGTAA
Found at i:10942 original size:32 final size:33
Alignment explanation
Indices: 10899--10960 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
10889 AGAAAAGAGT
* *
10899 AAAAAATAGT-AAAAATGGTATTCAGTAAAGGA
1 AAAAAAGAGTAAAAAATGGTATTCAATAAAGGA
10931 AAAAAAGAGTAAAAAATGGTATTCAATAAA
1 AAAAAAGAGTAAAAAATGGTATTCAATAAA
10961 AAAGTAAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 9 0.33
33 18 0.67
ACGTcount: A:0.60, C:0.03, G:0.16, T:0.21
Consensus pattern (33 bp):
AAAAAAGAGTAAAAAATGGTATTCAATAAAGGA
Found at i:10967 original size:25 final size:26
Alignment explanation
Indices: 10932--10989 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 26
10922 AGTAAAGGAA
*
10932 AAAAAGAGTAA-AAAATGG-TATTCAAT
1 AAAAA-AGTAAGAAAA-GGATAATCAAT
*
10958 AAAAAAGTAAGAAAAGGATAATCAGT
1 AAAAAAGTAAGAAAAGGATAATCAAT
10984 AAAAAA
1 AAAAAA
10990 AAGAGTAAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 7 0.25
26 21 0.75
ACGTcount: A:0.64, C:0.03, G:0.16, T:0.17
Consensus pattern (26 bp):
AAAAAAGTAAGAAAAGGATAATCAAT
Found at i:11030 original size:27 final size:27
Alignment explanation
Indices: 10930--11090 Score: 120
Period size: 25 Copynumber: 5.8 Consensus size: 27
10920 TCAGTAAAGG
10930 AAAAAAAGAGTAAAAAATGGT-ATTCA--
1 AAAAAAAGAGT-AAAAATGGTAATT-AGT
* * *
10956 ATAAAAA-AGTAAGAAAAGGATAATCAGT
1 AAAAAAAGAGTAA-AAATGG-TAATTAGT
*
10984 AAAAAAAAGAGTAAGAAAATGGTAATAAGT
1 -AAAAAAAGAGT-A-AAAATGGTAATTAGT
*
11014 AAAAAAAGAGTAAAAATAGTAATTAGT
1 AAAAAAAGAGTAAAAATGGTAATTAGT
11041 --AAAAAGAGTAAGAAA-GGTAATTAGT
1 AAAAAAAGAGTAA-AAATGGTAATTAGT
*
11066 AAAAGAAGAAGGTAGAAAATGGTAA
1 AAAAAAAG-A-GTA-AAAATGGTAA
11091 AAAGGGAGTA
Statistics
Matches: 109, Mismatches: 10, Indels: 28
0.74 0.07 0.19
Matches are distributed among these distances:
24 2 0.02
25 28 0.26
26 11 0.10
27 20 0.18
28 2 0.02
29 23 0.21
30 16 0.15
31 6 0.06
32 1 0.01
ACGTcount: A:0.61, C:0.01, G:0.20, T:0.18
Consensus pattern (27 bp):
AAAAAAAGAGTAAAAATGGTAATTAGT
Found at i:11085 original size:82 final size:84
Alignment explanation
Indices: 10930--11090 Score: 217
Period size: 83 Copynumber: 1.9 Consensus size: 84
10920 TCAGTAAAGG
*
10930 AAAAAAAGAGTAAAAAATGGTATTCAATAAAAAAGTAAGAAAAGGATAATCAGTAAAAAAAAGAG
1 AAAAAAAGAGTAAAAAATAGTATTCAATAAAAAAGTAAGAAAAGGATAATCAGTAAAAAAAAGAG
10995 TAAGAAAATGGTAATAAGT
66 TAAGAAAATGGTAATAAGT
* *
11014 AAAAAAAGAGT-AAAAATAGTAATT-AGTAAAAAGAGTAAG-AAAGG-TAATTAGTAAAAGAAGA
1 AAAAAAAGAGTAAAAAATAGT-ATTCAATAAAAA-AGTAAGAAAAGGATAATCAGTAAAA-AA-A
11075 AG-GT-AGAAAATGGTAA
62 AGAGTAAGAAAATGGTAA
11091 AAAGGGAGTA
Statistics
Matches: 70, Mismatches: 3, Indels: 10
0.84 0.04 0.12
Matches are distributed among these distances:
82 23 0.33
83 24 0.34
84 23 0.33
ACGTcount: A:0.61, C:0.01, G:0.20, T:0.18
Consensus pattern (84 bp):
AAAAAAAGAGTAAAAAATAGTATTCAATAAAAAAGTAAGAAAAGGATAATCAGTAAAAAAAAGAG
TAAGAAAATGGTAATAAGT
Found at i:12947 original size:53 final size:53
Alignment explanation
Indices: 12863--12966 Score: 190
Period size: 53 Copynumber: 2.0 Consensus size: 53
12853 ATTCGCTTTA
*
12863 TTGGGGGAACTCAACTGATTTTAGCTACTCCCATACGTAATCTAGACCACATT
1 TTGGGGGAACTCAACTGATTTTAACTACTCCCATACGTAATCTAGACCACATT
*
12916 TTGGGGGAACTCAACTGATTTTAACTGCTCCCATACGTAATCTAGACCACA
1 TTGGGGGAACTCAACTGATTTTAACTACTCCCATACGTAATCTAGACCACA
12967 AAAATGTGGC
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 49 1.00
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (53 bp):
TTGGGGGAACTCAACTGATTTTAACTACTCCCATACGTAATCTAGACCACATT
Done.