Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009328.1 Corchorus capsularis cultivar CVL-1 contig09349, 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: 16878
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.33
Found at i:3739 original size:32 final size:32
Alignment explanation
Indices: 3545--3738 Score: 144
Period size: 32 Copynumber: 6.4 Consensus size: 32
3535 ATAGTATCCT
* *
3545 TGTGCATCTCCCGCACACTATAATGATGTTCG
1 TGTGCATCTCCCGCAAACTATAATGATATTCG
* *
3577 TGTGCATCTCCCGCACAACGA-AAT-AT-TT-A
1 TGTGCATCTCCCGCA-AACTATAATGATATTCG
* * *
3606 TGTGCACTCTCCCACATAGTAT--TG-TA-T-G
1 TGTGCA-TCTCCCGCAAACTATAATGATATTCG
* * *
3634 TGTGCACCTCCCGCACACTATAATGATATACCG
1 TGTGCATCTCCCGCAAACTATAATGATAT-TCG
* * *
3667 TGTGCA-CTCCTGC-AA--ATAATGGTATTCT
1 TGTGCATCTCCCGCAAACTATAATGATATTCG
*
3695 TGTGCATCTCCCACAAACTATAATGATATTCG
1 TGTGCATCTCCCGCAAACTATAATGATATTCG
3727 TGTGCATCTCCC
1 TGTGCATCTCCC
3739 ATACAACGAA
Statistics
Matches: 125, Mismatches: 22, Indels: 30
0.71 0.12 0.17
Matches are distributed among these distances:
27 11 0.09
28 16 0.13
29 24 0.19
30 14 0.11
31 3 0.02
32 47 0.38
33 10 0.08
ACGTcount: A:0.25, C:0.28, G:0.16, T:0.31
Consensus pattern (32 bp):
TGTGCATCTCCCGCAAACTATAATGATATTCG
Found at i:3751 original size:150 final size:149
Alignment explanation
Indices: 3415--3830 Score: 600
Period size: 150 Copynumber: 2.8 Consensus size: 149
3405 CCCGCACATC
* *
3415 ATAATGATATACGTGTACATCTCCCGCACAACGAAATATCTATGTGCACTCCCACACATAGTACT
1 ATAATGATATTCGTGTGCATCTCCCGCACAACGAAATATCTATGTGCACTCCCACACATAGTACT
* ** * *
3480 GTATGTGTGCACCTCCCGCACACTATAATGATACACATTTATACTCCTGTACATAATAGTATCCT
66 GTATGTGTGCACCTCCCGCACACTATAATGATACACATGTGCACTCCTGCAAATAATAGTATCCT
* *
3545 TGTGCATCTCCCGCACACT
131 TGTGCATCTCCCACAAACT
* * *
3564 ATAATGATGTTCGTGTGCATCTCCCGCACAACGAAATATTTATGTGCACTCTCC-CACATAGTAT
1 ATAATGATATTCGTGTGCATCTCCCGCACAACGAAATATCTATGTGCACTC-CCACACATAGTAC
* * * *
3628 TGTATGTGTGCACCTCCCGCACACTATAATGATATACCGTGTGCACTCCTGCAAATAATGGTATT
65 TGTATGTGTGCACCTCCCGCACACTATAATGATACA-CATGTGCACTCCTGCAAATAATAGTATC
3693 CTTGTGCATCTCCCACAAACT
129 CTTGTGCATCTCCCACAAACT
** *
3714 ATAATGATATTCGTGTGCATCTCCCATACAACGAAATATCTATGTGCACTCCCGCACATAGTACT
1 ATAATGATATTCGTGTGCATCTCCCGCACAACGAAATATCTATGTGCACTCCCACACATAGTACT
* * *
3779 GCACGTGTGCACCTCCCGCACACTATAATGATACATCTTGTGCACTCCTGCA
66 GTATGTGTGCACCTCCCGCACACTATAATGATACA-CATGTGCACTCCTGCA
3831 TACTGTTTAT
Statistics
Matches: 238, Mismatches: 26, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
149 93 0.39
150 145 0.61
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (149 bp):
ATAATGATATTCGTGTGCATCTCCCGCACAACGAAATATCTATGTGCACTCCCACACATAGTACT
GTATGTGTGCACCTCCCGCACACTATAATGATACACATGTGCACTCCTGCAAATAATAGTATCCT
TGTGCATCTCCCACAAACT
Found at i:5600 original size:47 final size:48
Alignment explanation
Indices: 5547--5671 Score: 225
Period size: 47 Copynumber: 2.6 Consensus size: 48
5537 GAGCAACTTC
*
5547 AACTTCAAGATTGTTCAACTTCAACTTCAAAAGGATGGCC-AGAAAAA
1 AACTTCAAGATTGTTCAACTTCAACTTCAAAAGGATGGCCAAAAAAAA
5594 AACTTCAAGATTGTTCAACTTCAACTTCAAAAGGATGGCCAAAAAAAAA
1 AACTTCAAGATTGTTCAACTTCAACTTCAAAAGGATGGCC-AAAAAAAA
5643 AACTTCAAGATTGTTCAACTTCAACTTCA
1 AACTTCAAGATTGTTCAACTTCAACTTCA
5672 CCTAATGTGC
Statistics
Matches: 75, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
47 40 0.53
49 35 0.47
ACGTcount: A:0.42, C:0.20, G:0.12, T:0.26
Consensus pattern (48 bp):
AACTTCAAGATTGTTCAACTTCAACTTCAAAAGGATGGCCAAAAAAAA
Found at i:7846 original size:36 final size:36
Alignment explanation
Indices: 7818--7950 Score: 230
Period size: 36 Copynumber: 3.7 Consensus size: 36
7808 TATTGACTTC
7818 ACTTAATTACCCTGAATTAAGCCTTTTATTGACGCT
1 ACTTAATTACCCTGAATTAAGCCTTTTATTGACGCT
*
7854 ACTTAATTACCCTGAATTAGGCCTTTTATTGACGCT
1 ACTTAATTACCCTGAATTAAGCCTTTTATTGACGCT
*
7890 ACTTAATTACCCTGAATTAAGTCCATTTATTGACGCT
1 ACTTAATTACCCTGAATTAAG-CCTTTTATTGACGCT
*
7927 ACTTAATTACCCCGAATTAAGCCT
1 ACTTAATTACCCTGAATTAAGCCT
7951 ATGACTTGAC
Statistics
Matches: 91, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
36 57 0.63
37 34 0.37
ACGTcount: A:0.29, C:0.23, G:0.11, T:0.37
Consensus pattern (36 bp):
ACTTAATTACCCTGAATTAAGCCTTTTATTGACGCT
Found at i:7928 original size:37 final size:37
Alignment explanation
Indices: 7797--7947 Score: 220
Period size: 36 Copynumber: 4.2 Consensus size: 37
7787 CTCTTCTTAG
* *
7797 ATTAAGTTC-TTTATTGAC-TTCACTTAATTACCCTGA
1 ATTAAGTCCTTTTATTGACGCT-ACTTAATTACCCTGA
7833 ATTAAG-CCTTTTATTGACGCTACTTAATTACCCTGA
1 ATTAAGTCCTTTTATTGACGCTACTTAATTACCCTGA
*
7869 ATT-AGGCCTTTTATTGACGCTACTTAATTACCCTGA
1 ATTAAGTCCTTTTATTGACGCTACTTAATTACCCTGA
* *
7905 ATTAAGTCCATTTATTGACGCTACTTAATTACCCCGA
1 ATTAAGTCCTTTTATTGACGCTACTTAATTACCCTGA
7942 ATTAAG
1 ATTAAG
7948 CCTATGACTT
Statistics
Matches: 106, Mismatches: 5, Indels: 7
0.90 0.04 0.06
Matches are distributed among these distances:
35 3 0.03
36 66 0.62
37 37 0.35
ACGTcount: A:0.28, C:0.21, G:0.11, T:0.39
Consensus pattern (37 bp):
ATTAAGTCCTTTTATTGACGCTACTTAATTACCCTGA
Found at i:8199 original size:37 final size:37
Alignment explanation
Indices: 7959--8224 Score: 397
Period size: 37 Copynumber: 7.2 Consensus size: 37
7949 CTATGACTTG
* * *
7959 ACTTAATTTCCTTCCTTGAAATTAAGTCCTCTACTCT
1 ACTTAATTCCCTTCCTTGGAATCAAGTCCTCTACTCT
*
7996 ACTTAATTCCCTTCCTTGGAATCAAGTCATCTACTCT
1 ACTTAATTCCCTTCCTTGGAATCAAGTCCTCTACTCT
*
8033 ACTTAATTCCCTTCCTTGGAATCAAGTCCCCTACTCT
1 ACTTAATTCCCTTCCTTGGAATCAAGTCCTCTACTCT
*
8070 ACTTAATTCCCTTCCTTGGAATCAAGTCCCCTACTCT
1 ACTTAATTCCCTTCCTTGGAATCAAGTCCTCTACTCT
* *
8107 ACTTAATTCCATTCCTTGGAATCAAGTCCTGTACTCT
1 ACTTAATTCCCTTCCTTGGAATCAAGTCCTCTACTCT
* *
8144 ACTTAATTCCCTTCCTTGGAATCAAGTCCTTTGCTCT
1 ACTTAATTCCCTTCCTTGGAATCAAGTCCTCTACTCT
* * * * *
8181 ACTTAAGTCCCTTCCTTGGAACCAAGTCCTTTTCTTT
1 ACTTAATTCCCTTCCTTGGAATCAAGTCCTCTACTCT
8218 ACTTAAT
1 ACTTAAT
8225 CCCCGGAGGT
Statistics
Matches: 212, Mismatches: 17, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 212 1.00
ACGTcount: A:0.23, C:0.30, G:0.09, T:0.39
Consensus pattern (37 bp):
ACTTAATTCCCTTCCTTGGAATCAAGTCCTCTACTCT
Found at i:8292 original size:36 final size:36
Alignment explanation
Indices: 8234--8332 Score: 105
Period size: 36 Copynumber: 2.8 Consensus size: 36
8224 TCCCCGGAGG
* * *
8234 TTAAGTTTTTGTCTGATCTTACTTAATCATCTT-TG-GA
1 TTAAGTCTTTG-CTGATTTTACTTAAT--TCTTATGAAA
*
8271 TTAAGTCTTTGGTGATTTTACTTAATTCTTATGAAA
1 TTAAGTCTTTGCTGATTTTACTTAATTCTTATGAAA
*
8307 TTAAGTCTTTGCT-AATTTACTTAATT
1 TTAAGTCTTTGCTGATTTTACTTAATT
8333 ACCCTGAATT
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
34 4 0.07
35 14 0.26
36 26 0.48
37 10 0.19
ACGTcount: A:0.25, C:0.11, G:0.12, T:0.52
Consensus pattern (36 bp):
TTAAGTCTTTGCTGATTTTACTTAATTCTTATGAAA
Found at i:8471 original size:76 final size:76
Alignment explanation
Indices: 8380--8977 Score: 1047
Period size: 76 Copynumber: 7.9 Consensus size: 76
8370 CCTTCCTTGA
*
8380 AATTAAGTCTATGCTTGTCTTTACCTCATTTCCTTCAC-TGAAATTAAGTCTGTGCTTACTTTAC
1 AATTAAGTCTATGCTTGTCTTTACCTAATTTCCTTC-CTTGAAATTAAGTCTGTGCTTACTTTAC
*
8444 TTAATTACCCTG
65 TTAATTACCCCG
* *
8456 AATTAAGTCTATGCTTGTTTTTACCTAATTTCCTTCCTTGTAATTAAGTCTGTGCTTACTTTACT
1 AATTAAGTCTATGCTTGTCTTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTGCTTACTTTACT
*
8521 TAATTACCGCG
66 TAATTACCCCG
*
8532 AATTAAGTCTATGCTTGTCTTTACCTAATTTACTTCCTTGAAATTAAGTCTGTGCTTACTTTACT
1 AATTAAGTCTATGCTTGTCTTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTGCTTACTTTACT
8597 TAATTACCCCG
66 TAATTACCCCG
*
8608 AATTAAGTCTATACTTGTCTTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTGCTTACTTTACT
1 AATTAAGTCTATGCTTGTCTTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTGCTTACTTTACT
8673 TAATTACCCCG
66 TAATTACCCCG
*
8684 AATTAAGTATATGCTTGTCTTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTGCTTACTTTACT
1 AATTAAGTCTATGCTTGTCTTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTGCTTACTTTACT
8749 TAATTACCCCG
66 TAATTACCCCG
* *
8760 AATTAAGTATATGCTTGTCTTTACCTAATTTCCTTCCTTGAAATTAAGTTTGTGCTTACTTTACT
1 AATTAAGTCTATGCTTGTCTTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTGCTTACTTTACT
8825 TAATTACCCCG
66 TAATTACCCCG
8836 AATTAAGTCTATGCTTGTCTTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTGCTTACTTTACT
1 AATTAAGTCTATGCTTGTCTTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTGCTTACTTTACT
* * *
8901 TAGTTAACTCG
66 TAATTACCCCG
*
8912 AATTAAGT-TATGCTTGTTTTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTGCTTACTTTACT
1 AATTAAGTCTATGCTTGTCTTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTGCTTACTTTACT
8976 TA
66 TA
8978 GGCTCTGTTT
Statistics
Matches: 501, Mismatches: 20, Indels: 3
0.96 0.04 0.01
Matches are distributed among these distances:
75 58 0.12
76 443 0.88
ACGTcount: A:0.24, C:0.20, G:0.11, T:0.45
Consensus pattern (76 bp):
AATTAAGTCTATGCTTGTCTTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTGCTTACTTTACT
TAATTACCCCG
Found at i:10081 original size:41 final size:40
Alignment explanation
Indices: 9991--10131 Score: 201
Period size: 41 Copynumber: 3.5 Consensus size: 40
9981 ACTGCTTTTA
* * ** *
9991 CTTAATCACCTTGGATTAAAACCTTAACTAATCTGACTTT
1 CTTAATCGCCCTGGATTAAAACCTTAACTTGTTTGACTTT
10031 CTTAATCGCCCTGGATTAAAACCTTAACTGTGTTTGACTTT
1 CTTAATCGCCCTGGATTAAAACCTTAACT-TGTTTGACTTT
*
10072 CTTAATCGCCCTGGATTAAAACCTTAACTATGTTTGACCTT
1 CTTAATCGCCCTGGATTAAAACCTTAACT-TGTTTGACTTT
*
10113 CTTAATCGCCCTAGATTAA
1 CTTAATCGCCCTGGATTAA
10132 GACTTTACTT
Statistics
Matches: 92, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
40 27 0.29
41 65 0.71
ACGTcount: A:0.28, C:0.23, G:0.11, T:0.37
Consensus pattern (40 bp):
CTTAATCGCCCTGGATTAAAACCTTAACTTGTTTGACTTT
Found at i:16433 original size:13 final size:13
Alignment explanation
Indices: 16412--16446 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
16402 ATAATTATTG
*
16412 TTTGTTTTATTAA
1 TTTGCTTTATTAA
16425 TTTGCTTTATTAA
1 TTTGCTTTATTAA
16438 TTTGCTTTA
1 TTTGCTTTA
16447 GATTTAAGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.20, C:0.06, G:0.09, T:0.66
Consensus pattern (13 bp):
TTTGCTTTATTAA
Found at i:16462 original size:6 final size:6
Alignment explanation
Indices: 16443--16476 Score: 59
Period size: 6 Copynumber: 5.5 Consensus size: 6
16433 ATTAATTTGC
16443 TTTAGA TTTAAGA TTTAGA TTTAGA TTTAGA TTT
1 TTTAGA TTT-AGA TTTAGA TTTAGA TTTAGA TTT
16477 GCTTTGCTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 21 0.78
7 6 0.22
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.53
Consensus pattern (6 bp):
TTTAGA
Done.