Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012458.1 Corchorus olitorius cultivar O-4 contig12491, 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: 10738
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:7583 original size:27 final size:28
Alignment explanation
Indices: 7537--7597 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 28
7527 CCTTTTTTTC
*
7537 AAAT-ATATTTCTAAATTTCCATTATT-
1 AAATAATATTTCTAAATTTCCAATATTA
*
7563 AAATAATATTT-TAATTATTCCAATATTA
1 AAATAATATTTCTAAAT-TTCCAATATTA
7591 AAATAAT
1 AAATAAT
7598 GAAAATTTAG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 8 0.27
27 15 0.50
28 7 0.23
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (28 bp):
AAATAATATTTCTAAATTTCCAATATTA
Found at i:9055 original size:22 final size:22
Alignment explanation
Indices: 8947--9177 Score: 121
Period size: 22 Copynumber: 10.5 Consensus size: 22
8937 AAGGAGTACT
* *
8947 AAAATTTGATAGA-AGGTTATC
1 AAAATTTCATAAAGAGGTTATC
* * *
8968 -AAATCTCATAGAGTGGTTATC
1 AAAATTTCATAAAGAGGTTATC
* *
8989 -GAATTTCATAAAGATCAGATTATC
1 AAAATTTCATAAAG---AGGTTATC
* ** ***
9013 AAAATTTTATAGTGTTATTATC
1 AAAATTTCATAAAGAGGTTATC
9035 AAAATTTCA-AAACGAGGTTATC
1 AAAATTTCATAAA-GAGGTTATC
* * * *
9057 AAAATTACATAATGTGATTATC
1 AAAATTTCATAAAGAGGTTATC
* * * *
9079 AAAATTTCATAGAGGGGTCAAC
1 AAAATTTCATAAAGAGGTTATC
* * * *
9101 AAAATTTTATAGAGAGTTTATT
1 AAAATTTCATAAAGAGGTTATC
9123 AAAATTTCATAAAGAGGTTATC
1 AAAATTTCATAAAGAGGTTATC
* * * *
9145 AAATTTTCA-AAATGTGATTACC
1 AAAATTTCATAAA-GAGGTTATC
9167 AAAATTTCATA
1 AAAATTTCATA
9178 GTGGTATTTT
Statistics
Matches: 155, Mismatches: 46, Indels: 16
0.71 0.21 0.07
Matches are distributed among these distances:
20 10 0.06
21 21 0.14
22 106 0.68
23 3 0.02
24 6 0.04
25 9 0.06
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.35
Consensus pattern (22 bp):
AAAATTTCATAAAGAGGTTATC
Found at i:9059 original size:44 final size:44
Alignment explanation
Indices: 8990--9177 Score: 175
Period size: 44 Copynumber: 4.2 Consensus size: 44
8980 GTGGTTATCG
* * *
8990 AATTTCATAAAGATCAGATTATCAAAATTTTATAGTGTTATTATCAA
1 AATTTCATAAAG---AGGTTATCAAAATTTTATAATGTGATTATCAA
**
9037 AATTTCA-AAACGAGGTTATCAAAATTACATAATGTGATTATCAA
1 AATTTCATAAA-GAGGTTATCAAAATTTTATAATGTGATTATCAA
* * * * * * *
9081 AATTTCATAGAGGGGTCAACAAAATTTTATAGA-GAGTTTATTAA
1 AATTTCATAAAGAGGTTATCAAAATTTTATA-ATGTGATTATCAA
* *
9125 AATTTCATAAAGAGGTTATC-AAATTTTCAAAATGTGATTACCAA
1 AATTTCATAAAGAGGTTATCAAAATTTT-ATAATGTGATTATCAA
9169 AATTTCATA
1 AATTTCATA
9178 GTGGTATTTT
Statistics
Matches: 113, Mismatches: 23, Indels: 13
0.76 0.15 0.09
Matches are distributed among these distances:
43 8 0.07
44 91 0.81
45 3 0.03
46 3 0.03
47 8 0.07
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.36
Consensus pattern (44 bp):
AATTTCATAAAGAGGTTATCAAAATTTTATAATGTGATTATCAA
Found at i:9104 original size:88 final size:88
Alignment explanation
Indices: 9012--9178 Score: 239
Period size: 88 Copynumber: 1.9 Consensus size: 88
9002 ATCAGATTAT
* * *
9012 CAAAATTTTATAGTG-TTATTATCAAAATTTCA-AAACGAGGTTATCAAAATTACATAATGTGAT
1 CAAAATTTTATAGAGAGT-TTATCAAAATTTCATAAA-GAGGTTATCAAAATTACAAAATGTGAT
*
9075 TATCAAAATTTCATAGAGGGGTCAA
64 TACCAAAATTTCATAGAGGGGTCAA
* * *
9100 CAAAATTTTATAGAGAGTTTATTAAAATTTCATAAAGAGGTTATCAAATTTTCAAAATGTGATTA
1 CAAAATTTTATAGAGAGTTTATCAAAATTTCATAAAGAGGTTATCAAAATTACAAAATGTGATTA
9165 CCAAAATTTCATAG
66 CCAAAATTTCATAG
9179 TGGTATTTTT
Statistics
Matches: 70, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
88 66 0.94
89 4 0.06
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.35
Consensus pattern (88 bp):
CAAAATTTTATAGAGAGTTTATCAAAATTTCATAAAGAGGTTATCAAAATTACAAAATGTGATTA
CCAAAATTTCATAGAGGGGTCAA
Found at i:9219 original size:22 final size:21
Alignment explanation
Indices: 9193--9509 Score: 154
Period size: 22 Copynumber: 15.0 Consensus size: 21
9183 ATTTTTGGGG
9193 AGGTTATCAAAATTTCATAGT
1 AGGTTATCAAAATTTCATAGT
* * *
9214 ATGGTTA-CCAAA-TT-A-GGA
1 A-GGTTATCAAAATTTCATAGT
* * *
9232 AGGTTATTAAACTTTTACTA-T
1 AGGTTATCAAAATTTCA-TAGT
* * *
9253 GGAGTTATCAAAATTTCA-GGC
1 AG-GTTATCAAAATTTCATAGT
* *
9274 AGGATATCAAAATTTCATATGA
1 AGGTTATCAAAATTTCATA-GT
9296 AGGTTATCAAAATTTCATAGTTT
1 AGGTTATCAAAATTTCATAG--T
* *
9319 A-GTTTTCAAAATTTCATAGG
1 AGGTTATCAAAATTTCATAGT
9339 AGGATTATCAAAATTTCATAGT
1 AGG-TTATCAAAATTTCATAGT
* * *
9361 ATGTAGATCAAAATTTCATAGGG
1 AGGT-TATCAAAATTTCATA-GT
* * *
9384 AGATTAACAAAATTTCATAAT
1 AGGTTATCAAAATTTCATAGT
*
9405 GAGGTTATCAGAA-TT--T-GT
1 -AGGTTATCAAAATTTCATAGT
* *
9423 A-GTTATCAAGATTTCATAAGG
1 AGGTTATCAAAATTTCAT-AGT
* * * *
9444 AGATTATAAAAATTTTATAAGG
1 AGGTTATCAAAATTTCAT-AGT
* * *
9466 AGATTTATCAAAATTTTATAGGA
1 AG-GTTATCAAAATTTCATA-GT
9489 AGGTTTATCAAAATTTCATAG
1 AGG-TTATCAAAATTTCATAG
9510 CTTTCAGAGT
Statistics
Matches: 221, Mismatches: 49, Indels: 51
0.69 0.15 0.16
Matches are distributed among these distances:
16 8 0.04
17 8 0.04
18 5 0.02
19 5 0.02
20 18 0.08
21 14 0.06
22 127 0.57
23 36 0.16
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.36
Consensus pattern (21 bp):
AGGTTATCAAAATTTCATAGT
Found at i:9395 original size:66 final size:66
Alignment explanation
Indices: 9227--9509 Score: 200
Period size: 66 Copynumber: 4.4 Consensus size: 66
9217 GTTACCAAAT
* * * * *
9227 TAGGAAGGTTATTAAACTTTTACTATGGAGTTATCAAAATTTC---AGGCAGGA-TATCAAAATT
1 TAGGAAGGTTATCAAAATTTCA-TAGGGAGTTAACAAAATTTCATAAGG-AGGATTATCAAAATT
9288 TCA
64 TCA
* ** **
9291 TATGAAGGTTATCAAAATTTCATAGTTTAGTTTTCAAAATTTCAT-AGGAGGATTATCAAAATTT
1 TAGGAAGGTTATCAAAATTTCATAG-GGAGTTAACAAAATTTCATAAGGAGGATTATCAAAATTT
9355 CA
65 CA
* * * * *
9357 TA-GTATGTAGATCAAAATTTCATAGGGAGATTAACAAAATTTCATAATGAGG-TTATCAGAA-T
1 TAGGAAGGT-TATCAAAATTTCATAGGGAG-TTAACAAAATTTCATAAGGAGGATTATCAAAATT
9419 T--
64 TCA
* * * *
9420 T--GTA-GTTATCAAGATTTCATAAGGAGATTATA-AAAATTTTATAAGGA-GATTTATCAAAAT
1 TAGGAAGGTTATCAAAATTTCATAGGGAG-TTA-ACAAAATTTCATAAGGAGGA-TTATCAAAAT
*
9480 TTTA
63 TTCA
9484 TAGGAAGGTTTATCAAAATTTCATAG
1 TAGGAAGG-TTATCAAAATTTCATAG
9510 CTTTCAGAGT
Statistics
Matches: 176, Mismatches: 26, Indels: 30
0.76 0.11 0.13
Matches are distributed among these distances:
59 1 0.01
60 34 0.19
61 11 0.06
62 5 0.03
63 3 0.02
64 33 0.19
65 12 0.07
66 56 0.32
67 6 0.03
68 15 0.09
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (66 bp):
TAGGAAGGTTATCAAAATTTCATAGGGAGTTAACAAAATTTCATAAGGAGGATTATCAAAATTTC
A
Found at i:9478 original size:23 final size:23
Alignment explanation
Indices: 9425--9504 Score: 101
Period size: 23 Copynumber: 3.5 Consensus size: 23
9415 GAATTTGTAG
* *
9425 TTATCAAGATTTCATAAGGAGA-
1 TTATCAAAATTTTATAAGGAGAT
*
9447 TTATAAAAATTTTATAAGGAGAT
1 TTATCAAAATTTTATAAGGAGAT
*
9470 TTATCAAAATTTTAT-AGGAAGGT
1 TTATCAAAATTTTATAAGG-AGAT
9493 TTATCAAAATTT
1 TTATCAAAATTT
9505 CATAGCTTTC
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
22 22 0.43
23 29 0.57
ACGTcount: A:0.42, C:0.05, G:0.14, T:0.39
Consensus pattern (23 bp):
TTATCAAAATTTTATAAGGAGAT
Found at i:9582 original size:22 final size:22
Alignment explanation
Indices: 9557--9616 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 22
9547 TTTTAAATTT
*
9557 TCATAATGTGGTTATCAATATA
1 TCATAATGTGGTTATCAACATA
* *
9579 TCAT-ATAGAGGTTATCAACATC
1 TCATAAT-GTGGTTATCAACATA
*
9601 TCATAGTGTTGGTTAT
1 TCATAATG-TGGTTAT
9617 TAAAATTTCA
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
21 2 0.07
22 21 0.70
23 7 0.23
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.40
Consensus pattern (22 bp):
TCATAATGTGGTTATCAACATA
Found at i:9704 original size:22 final size:22
Alignment explanation
Indices: 9679--9724 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
9669 CTTAGGGAGA
* *
9679 TTAACAAAATTTCATAAGAAGG
1 TTAAAAAAATTTCATAAAAAGG
*
9701 TTAAAAAAATTTTATAAAAAGG
1 TTAAAAAAATTTCATAAAAAGG
9723 TT
1 TT
9725 CTCGAAATTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.52, C:0.04, G:0.11, T:0.33
Consensus pattern (22 bp):
TTAAAAAAATTTCATAAAAAGG
Found at i:9910 original size:2 final size:2
Alignment explanation
Indices: 9903--9938 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
9893 GCTAATACTA
9903 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9939 TATTGAATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10533 original size:48 final size:48
Alignment explanation
Indices: 10481--10586 Score: 106
Period size: 48 Copynumber: 2.2 Consensus size: 48
10471 AATCTTGGAT
* *
10481 ATTTTGGTCAATTTCGAT-CACCATCGGTCATGATGATTAACCTTGGCC
1 ATTTTAGTCAATTTCG-TCCACCATAGGTCATGATGATTAACCTTGGCC
** * ** * *
10529 ATTTTAACCAATTTTGTCCACCATAGGTTGTGATGGTTAGCCTTGGCC
1 ATTTTAGTCAATTTCGTCCACCATAGGTCATGATGATTAACCTTGGCC
*
10577 ATTTTTGTCA
1 ATTTTAGTCA
10587 CCTTGGTTGT
Statistics
Matches: 45, Mismatches: 12, Indels: 2
0.76 0.20 0.03
Matches are distributed among these distances:
47 1 0.02
48 44 0.98
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.39
Consensus pattern (48 bp):
ATTTTAGTCAATTTCGTCCACCATAGGTCATGATGATTAACCTTGGCC
Found at i:10597 original size:37 final size:39
Alignment explanation
Indices: 10535--10617 Score: 116
Period size: 37 Copynumber: 2.2 Consensus size: 39
10525 GGCCATTTTA
*
10535 ACCAATTTTGTCCACCATAGGTTGTGATGGTTAGCCTTG
1 ACCATTTTTGTCCACCATAGGTTGTGATGGTTAGCCTTG
* * *
10574 GCCATTTTTGT-CACC-TTGGTTGTGGTGGTTAGCCTTG
1 ACCATTTTTGTCCACCATAGGTTGTGATGGTTAGCCTTG
10611 ACCATTT
1 ACCATTT
10618 GGGCCAATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
37 26 0.67
38 4 0.10
39 9 0.23
ACGTcount: A:0.16, C:0.20, G:0.24, T:0.40
Consensus pattern (39 bp):
ACCATTTTTGTCCACCATAGGTTGTGATGGTTAGCCTTG
Done.