Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014324.1 Corchorus olitorius cultivar O-4 contig14357, 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: 5004
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38
Found at i:213 original size:51 final size:50
Alignment explanation
Indices: 112--213 Score: 125
Period size: 51 Copynumber: 2.0 Consensus size: 50
102 GTTCATCAAA
* **
112 TTTTCCTTGTTTAAATCTTGTCTCAGGACAAACAAACACTCTTTTAGTGT
1 TTTTCCTTGTTTAAATCTTGTCTCAGGACAAACAAACACTCGTACAGTGT
* * *
162 TTTTCTCTTGTTTCAATCTTGTCTCCGGACATACAAACACT-GTACACGTGT
1 TTTTC-CTTGTTTAAATCTTGTCTCAGGACAAACAAACACTCGTACA-GTGT
213 T
1 T
214 CTTCGTTCAG
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
50 7 0.16
51 37 0.84
ACGTcount: A:0.24, C:0.23, G:0.13, T:0.41
Consensus pattern (50 bp):
TTTTCCTTGTTTAAATCTTGTCTCAGGACAAACAAACACTCGTACAGTGT
Found at i:595 original size:22 final size:22
Alignment explanation
Indices: 560--796 Score: 162
Period size: 22 Copynumber: 10.7 Consensus size: 22
550 ATATAAAAGG
*
560 TTATC-AAATCTCATAGAGTGA
1 TTATCAAAATTTCATAGAGTGA
*
581 TTATCGAAATTTCATAGAGATCAGA
1 TTATCAAAATTTCATAGAG-T--GA
*
606 TTATCAAAATTTACA-AGA-AGA
1 TTATCAAAATTT-CATAGAGTGA
*
627 TTATCAAAATTTCATAGTATTG-
1 TTATCAAAATTTCATAG-AGTGA
* * * *
649 TTATCAAAATTTCAAAGCGAGG
1 TTATCAAAATTTCATAGAGTGA
*
671 TTATCAAAATTACATA-ATGTGA
1 TTATCAAAATTTCATAGA-GTGA
* *
693 TTATCAAAATTTCATAGAGGGG
1 TTATCAAAATTTCATAGAGTGA
* * * * * *
715 TCAACATAATTTTATAGAGAGG
1 TTATCAAAATTTCATAGAGTGA
* * *
737 TTATCAAAATTTCATAAAGAGG
1 TTATCAAAATTTCATAGAGTGA
* *
759 TTATCAAATTTTCA-AAATGTGA
1 TTATCAAAATTTCATAGA-GTGA
*
781 TTACCAAAATTTCATA
1 TTATCAAAATTTCATA
797 TTGGTATTTC
Statistics
Matches: 172, Mismatches: 31, Indels: 24
0.76 0.14 0.11
Matches are distributed among these distances:
20 2 0.01
21 25 0.15
22 123 0.72
23 4 0.02
25 16 0.09
26 2 0.01
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.34
Consensus pattern (22 bp):
TTATCAAAATTTCATAGAGTGA
Found at i:925 original size:22 final size:22
Alignment explanation
Indices: 897--1409 Score: 117
Period size: 22 Copynumber: 23.6 Consensus size: 22
887 TTAGGGAGGA
897 TATCAAAATTTCATATGAAGGT
1 TATCAAAATTTCATATGAAGGT
**
919 TATCAAAATTTCATAGTTTA-GT
1 TATCAAAATTTCATA-TGAAGGT
* * *
941 T-TGCAAAATTTCTTAGGAAGAT
1 TAT-CAAAATTTCATATGAAGGT
*
963 TAACAAAATTTCATAATG-AGGT
1 TATCAAAATTTCAT-ATGAAGGT
** * *
985 TATCAAAAAATCATAAGGAGGT
1 TATCAAAATTTCATATGAAGGT
*
1007 TATCAAAA--T--T-TGTA-GT
1 TATCAAAATTTCATATGAAGGT
* * * *
1023 TATCAAGATTCCATAAGGAGGT
1 TATCAAAATTTCATATGAAGGT
* * *
1045 TATCAAAATTTTATAGGGAGGTT
1 TATCAAAATTTCATATGAAGG-T
*
1068 TATCAAAATATT-ATAGGAAGGTT
1 TATCAAAAT-TTCATATGAAGG-T
* *
1091 TATCAAAGTTT-A-GTG-AGGT
1 TATCAAAATTTCATATGAAGGT
* * * *
1110 TATCACAATTTTATAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
* * *
1132 TATCGAAATTCCAGAGTGTAA--T
1 TATCAAAATTTCATA-TG-AAGGT
* *
1154 TA-CTAACAA-TTCATATGGACGT
1 TATC-AA-AATTTCATATGAAGGT
* * * * *
1176 TTTTAAATTTTCATAACG-TGGT
1 TATCAAAATTTCAT-ATGAAGGT
* * *
1198 TATCAATATATCATATGGAGGT
1 TATCAAAATTTCATATGAAGGT
* * **
1220 TATCAACATCTCATAGTGTTGGT
1 TATCAAAATTTCATA-TGAAGGT
1243 TATCAAAATTTCAT-TGGGAA-GT
1 TATCAAAATTTCATAT--GAAGGT
1265 TATCAAAATTTCATAGTG-A-GT
1 TATCAAAATTTCATA-TGAAGGT
* * *
1286 CT-TCAAAATTTCTTAGGGAGGT
1 -TATCAAAATTTCATATGAAGGT
* * *
1308 TAACAAAATTTCACAAGAAGGT
1 TATCAAAATTTCATATGAAGGT
** *
1330 TAAAAAAATTT-ATA-AAGAGGT
1 TATCAAAATTTCATATGA-AGGT
* * * * *
1351 TCTCGAAATTCCATA-GTATCGTT
1 TATCAAAATTTCATATG-A-AGGT
* * *
1374 TATTAAAATTTCATAGGAAAGT
1 TATCAAAATTTCATATGAAGGT
*
1396 TAACAAAATTTCAT
1 TATCAAAATTTCAT
1410 GAGGTCATCA
Statistics
Matches: 358, Mismatches: 93, Indels: 80
0.67 0.18 0.15
Matches are distributed among these distances:
16 9 0.03
17 2 0.01
18 1 0.00
19 10 0.03
20 9 0.03
21 43 0.12
22 211 0.59
23 69 0.19
24 4 0.01
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (22 bp):
TATCAAAATTTCATATGAAGGT
Found at i:1073 original size:23 final size:22
Alignment explanation
Indices: 846--1125 Score: 113
Period size: 22 Copynumber: 13.1 Consensus size: 22
836 GTTACCGAAT
* * *
846 TAGGAAGGTTATTAAACTTTTA
1 TAGGGAGGTTATCAAAATTTTA
* *
868 TTATGGA-GTAATCAAAA-TTT-
1 -TAGGGAGGTTATCAAAATTTTA
* *
888 TAGGGAGGATATCAAAATTTCA
1 TAGGGAGGTTATCAAAATTTTA
* * *
910 TATGAAGGTTATCAAAATTTCA
1 TAGGGAGGTTATCAAAATTTTA
**
932 TAGTTTA-GTT-TGCAAAATTTCT-
1 TAG-GGAGGTTAT-CAAAATTT-TA
* * * *
954 TAGGAAGATTAACAAAATTTCA
1 TAGGGAGGTTATCAAAATTTTA
** ** *
976 TAATGAGGTTATCAAAAAATCA
1 TAGGGAGGTTATCAAAATTTTA
*
998 TAAGGAGGTTATCAAAA--TT-
1 TAGGGAGGTTATCAAAATTTTA
* * **
1017 T--GTA-GTTATCAAGATTCCA
1 TAGGGAGGTTATCAAAATTTTA
*
1036 TAAGGAGGTTATCAAAATTTTA
1 TAGGGAGGTTATCAAAATTTTA
*
1058 TAGGGAGGTTTATCAAAATATTA
1 TAGGGAGG-TTATCAAAATTTTA
* *
1081 TAGGAAGGTTTATC-AAA-GTT-
1 TAGGGAGG-TTATCAAAATTTTA
* *
1101 TAGTGAGGTTATCACAATTTTA
1 TAGGGAGGTTATCAAAATTTTA
1123 TAG
1 TAG
1126 TGTGATTATC
Statistics
Matches: 192, Mismatches: 46, Indels: 39
0.69 0.17 0.14
Matches are distributed among these distances:
16 9 0.05
17 2 0.01
19 12 0.06
20 17 0.09
21 13 0.07
22 108 0.56
23 31 0.16
ACGTcount: A:0.39, C:0.07, G:0.18, T:0.36
Consensus pattern (22 bp):
TAGGGAGGTTATCAAAATTTTA
Found at i:1256 original size:23 final size:23
Alignment explanation
Indices: 1021--1320 Score: 120
Period size: 22 Copynumber: 13.7 Consensus size: 23
1011 AAAATTTGTA
* * *
1021 GTTATCAAGATTCCATA-AGGAG
1 GTTATCAAAATTTCATAGTGGAG
*
1043 GTTATCAAAATTTTATAG-GGAG
1 GTTATCAAAATTTCATAGTGGAG
*
1065 GTTTATCAAAATATT-ATAG-GAAG
1 G-TTATCAAAAT-TTCATAGTGGAG
*
1088 GTTTATC-AAAGTT--TAGT-GAG
1 G-TTATCAAAATTTCATAGTGGAG
* *
1108 GTTATCACAATTTTATAGTGTGA-
1 GTTATCAAAATTTCATAGTG-GAG
* * * *
1131 -TTATCGAAATTCCAGAGTGTA-
1 GTTATCAAAATTTCATAGTGGAG
* *
1152 ATTA-CTAACAA-TTCATA-TGGAC
1 GTTATC-AA-AATTTCATAGTGGAG
* * * ** *
1174 GTTTTTAAATTTTCATA-ACGTG
1 GTTATCAAAATTTCATAGTGGAG
* *
1196 GTTATCAATATATCATA-TGGAG
1 GTTATCAAAATTTCATAGTGGAG
* * **
1218 GTTATCAACATCTCATAGTGTTG
1 GTTATCAAAATTTCATAGTGGAG
* *
1241 GTTATCAAAATTTCATTG-GGAA
1 GTTATCAAAATTTCATAGTGGAG
1263 GTTATCAAAATTTCATAGT-GA-
1 GTTATCAAAATTTCATAGTGGAG
*
1284 GTCT-TCAAAATTTCTTAG-GGAG
1 GT-TATCAAAATTTCATAGTGGAG
*
1306 GTTAACAAAATTTCA
1 GTTATCAAAATTTCA
1321 CAAGAAGGTT
Statistics
Matches: 209, Mismatches: 48, Indels: 42
0.70 0.16 0.14
Matches are distributed among these distances:
19 5 0.02
20 10 0.05
21 26 0.12
22 120 0.57
23 44 0.21
24 4 0.02
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.37
Consensus pattern (23 bp):
GTTATCAAAATTTCATAGTGGAG
Found at i:1267 original size:45 final size:45
Alignment explanation
Indices: 1194--1282 Score: 117
Period size: 45 Copynumber: 2.0 Consensus size: 45
1184 TTTCATAACG
* * *
1194 TGGTTATCAATATATCATATGGAGGTTATCAACATCTCATAGTGT
1 TGGTTATCAAAATATCATATGGAAGTTATCAAAATCTCATAGTGT
* *
1239 TGGTTATCAAAATTTCAT-TGGGAAGTTATCAAAATTTCATAGTG
1 TGGTTATCAAAATATCATAT-GGAAGTTATCAAAATCTCATAGTG
1283 AGTCTTCAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
44 1 0.03
45 37 0.97
ACGTcount: A:0.33, C:0.11, G:0.18, T:0.38
Consensus pattern (45 bp):
TGGTTATCAAAATATCATATGGAAGTTATCAAAATCTCATAGTGT
Found at i:3380 original size:25 final size:29
Alignment explanation
Indices: 3334--3387 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 29
3324 ATAATAAATA
3334 AACTACATAAACTTAAACTTTTTAATATT
1 AACTACATAAACTTAAACTTTTTAATATT
3363 AACTACAT-AAC-T-AA-TTTTTAATATT
1 AACTACATAAACTTAAACTTTTTAATATT
3388 TTTTCTCACA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 11 0.44
26 2 0.08
27 1 0.04
28 3 0.12
29 8 0.32
ACGTcount: A:0.44, C:0.13, G:0.00, T:0.43
Consensus pattern (29 bp):
AACTACATAAACTTAAACTTTTTAATATT
Done.