Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009976.1 Corchorus capsularis cultivar CVL-1 contig09997, 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: 19529
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Found at i:1002 original size:87 final size:87
Alignment explanation
Indices: 890--1268 Score: 321
Period size: 87 Copynumber: 4.4 Consensus size: 87
880 ATGGTTACCT
** *
890 AAATTTCATA-TGGAGGTTACCAAAATTTCATTGTGAGGTTACCAAATTTCATAGGGAGACTACA
1 AAATTTCATAGT-GAGGTTACCAAAATTTCATAATGAGGTTACCAAATTTCATAGGG-GATTACA
*
954 AAAATTTCATACCG-AGCTTA-TAA
64 AAAATTTCATA-AGAAGCTTACTAA
* * * * *
977 AAATTTAATTGTGAGGTTACCAAAATTTCATAA-GGGGTCACCCAAATTTCATTGTGAGG-TTAC
1 AAATTTCATAGTGAGGTTACCAAAATTTCATAATGAGGTTA-CCAAATTTCATAG-G-GGATTAC
* *
1040 AAAAATTTCATAGTGCAG-TTACT-A
63 AAAAATTTCATA-AGAAGCTTACTAA
* * * * * *
1064 AAATATCATAGTG-GGTAACCAAAATTTC-TTATGGAGGTTTCCAAAATTTCATAGGGGGTTACT
1 AAATTTCATAGTGAGGTTACCAAAATTTCATAAT-GAGGTTACC-AAATTTCATAGGGGATTACA
* *
1127 AAAATTTCATAAGAAGCTTACCAC
64 AAAATTTCATAAGAAGCTTACTAA
* * * * * *
1151 AATTTTCATACT-ATCGTTACCAAAATTTCACAATGAGGTTGCCAAATTTCATAAGGGATTACAA
1 AAATTTCATAGTGA-GGTTACCAAAATTTCATAATGAGGTTACCAAATTTCATAGGGGATTACAA
* * *
1215 AAATTTCATAATAAGGTTAC-CA
65 AAATTTCATAAGAAGCTTACTAA
* *
1237 AAATTTCATAGTTAGCTTACCAAAATTTCATA
1 AAATTTCATAGTGAGGTTACCAAAATTTCATA
1269 GTTAGGTTCA
Statistics
Matches: 232, Mismatches: 44, Indels: 33
0.75 0.14 0.11
Matches are distributed among these distances:
85 7 0.03
86 66 0.28
87 129 0.56
88 27 0.12
89 3 0.01
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (87 bp):
AAATTTCATAGTGAGGTTACCAAAATTTCATAATGAGGTTACCAAATTTCATAGGGGATTACAAA
AATTTCATAAGAAGCTTACTAA
Found at i:1044 original size:65 final size:64
Alignment explanation
Indices: 890--1409 Score: 257
Period size: 65 Copynumber: 7.9 Consensus size: 64
880 ATGGTTACCT
* * *
890 AAATTTCATATG-GAGGTTACCAAAATTTCATTGTGAGGTTACC-AAATTTCATAGGGAGACTAC
1 AAATTTCAT-TGTGAGGTTACAAAAATTTCATAGTGAGGTTACCAAAATTTCATAGGG-GTC-AC
*
953 AA
63 CA
*** * * * * *
955 AAATTTCATACCGAGCTTATAAAAATTTAATTGTGAGGTTACCAAAATTTCATAAGGGGTCACCC
1 AAATTTCATTGTGAGGTTACAAAAATTTCATAGTGAGGTTACCAAAATTTCAT-AGGGGTCACCA
* * *
1020 AAATTTCATTGTGAGGTTACAAAAATTTCATAGTGCA-GTTACTAAAATATCATAGTGGGTAACC
1 AAATTTCATTGTGAGGTTACAAAAATTTCATAGTG-AGGTTACCAAAATTTCATAG-GGGTCACC
1084 A
64 A
* * * * * * * *
1085 AAATTTC-TTATGGAGGTTTCCAAAATTTCATAG-GGGGTTACTAAAATTTCATAAGAAGCTTAC
1 AAATTTCATTGT-GAGGTTACAAAAATTTCATAGTGAGGTTACCAAAATTTCAT-AG-GGGTCAC
1148 CA
63 CA
* ** * * * * * * *
1150 CAATTTTCATACT-ATCGTTACCAAAATTTCACAATGAGGTTGCC-AAATTTCATAAGGGATTAC
1 -AAATTTCATTGTGA-GGTTACAAAAATTTCATAGTGAGGTTACCAAAATTTCAT-AGGGGTCAC
*
1213 AA
63 CA
** * * * * *
1215 AAATTTCATAATAAGGTTACCAAAATTTCATAGTTAGCTTACCAAAATTTCATAGTTAGGTTCAC
1 AAATTTCATTGTGAGGTTACAAAAATTTCATAGTGAGGTTACCAAAATTTCATAG---GGGTCAC
*
1280 TAAAAAAAAA
63 --------CA
** ** * * * *
1290 AAAAATCATACTTAGGTTATC-AAAATTTCATAGTCAAGTTACCAAAATTTCATAGGAAGGTTAC
1 AAATTTCATTGTGAGGTTA-CAAAAATTTCATAGTGAGGTTACCAAAATTTCATAGG--GGTCAC
1354 CA
63 CA
* * * *
1356 AAATATCATAGTGAGGTTAC-AAAATTTCATAGGGAGGTTACCAAAATTTTATAG
1 AAATTTCATTGTGAGGTTACAAAAATTTCATAGTGAGGTTACCAAAATTTCATAG
1410 TCAGGTTACC
Statistics
Matches: 358, Mismatches: 69, Indels: 56
0.74 0.14 0.12
Matches are distributed among these distances:
64 56 0.16
65 169 0.47
66 62 0.17
67 17 0.05
72 1 0.00
74 4 0.01
75 48 0.13
76 1 0.00
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.32
Consensus pattern (64 bp):
AAATTTCATTGTGAGGTTACAAAAATTTCATAGTGAGGTTACCAAAATTTCATAGGGGTCACCA
Found at i:1088 original size:43 final size:43
Alignment explanation
Indices: 1041--1137 Score: 106
Period size: 43 Copynumber: 2.3 Consensus size: 43
1031 TGAGGTTACA
* *
1041 AAAATTTCATAGTGCA-GTTACTAAAATATCATAGTGGGTAACC
1 AAAATTTCATA-TGCAGGTTACCAAAATATCATAGGGGGTAACC
* * * * * *
1084 AAAATTTCTTATGGAGGTTTCCAAAATTTCATAGGGGGTTACT
1 AAAATTTCATATGCAGGTTACCAAAATATCATAGGGGGTAACC
1127 AAAATTTCATA
1 AAAATTTCATA
1138 AGAAGCTTAC
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
42 3 0.07
43 41 0.93
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.34
Consensus pattern (43 bp):
AAAATTTCATATGCAGGTTACCAAAATATCATAGGGGGTAACC
Found at i:1269 original size:22 final size:22
Alignment explanation
Indices: 882--1276 Score: 276
Period size: 22 Copynumber: 18.2 Consensus size: 22
872 TTGTTGATAT
*
882 GGTTACCTAAATTTCATA-TGGA
1 GGTTACCAAAATTTCATAGT-GA
*
904 GGTTACCAAAATTTCATTGTGA
1 GGTTACCAAAATTTCATAGTGA
*
926 GGTTACC-AAATTTCATAGGGA
1 GGTTACCAAAATTTCATAGTGA
** * **
947 GACTACAAAAATTTCATACCGA
1 GGTTACCAAAATTTCATAGTGA
* ** * *
969 GCTTATAAAAATTTAATTGTGA
1 GGTTACCAAAATTTCATAGTGA
991 GGTTACCAAAATTTCATAAG-G-
1 GGTTACCAAAATTTCAT-AGTGA
* * *
1012 GGTCACCCAAATTTCATTGTGA
1 GGTTACCAAAATTTCATAGTGA
*
1034 GGTTACAAAAATTTCATAGTGCA
1 GGTTACCAAAATTTCATAGTG-A
* *
1057 -GTTACTAAAATATCATAGTG-
1 GGTTACCAAAATTTCATAGTGA
* *
1077 GGTAACCAAAATTTCTTA-TGGA
1 GGTTACCAAAATTTCATAGT-GA
* *
1099 GGTTTCCAAAATTTCATAG-GG
1 GGTTACCAAAATTTCATAGTGA
* *
1120 GGTTACTAAAATTTCATAAG-AA
1 GGTTACCAAAATTTCAT-AGTGA
* * *
1142 GCTTACCACAATTTTCATACT-A
1 GGTTACCA-AAATTTCATAGTGA
* * *
1164 TCGTTACCAAAATTTCACAATGA
1 -GGTTACCAAAATTTCATAGTGA
*
1187 GGTTGCC-AAATTTCATAAG-G-
1 GGTTACCAAAATTTCAT-AGTGA
* * * *
1207 GATTACAAAAATTTCATAATAA
1 GGTTACCAAAATTTCATAGTGA
*
1229 GGTTACCAAAATTTCATAGTTA
1 GGTTACCAAAATTTCATAGTGA
* *
1251 GCTTACCAAAATTTCATAGTTA
1 GGTTACCAAAATTTCATAGTGA
1273 GGTT
1 GGTT
1277 CACTAAAAAA
Statistics
Matches: 288, Mismatches: 66, Indels: 38
0.73 0.17 0.10
Matches are distributed among these distances:
20 7 0.02
21 80 0.28
22 183 0.64
23 18 0.06
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (22 bp):
GGTTACCAAAATTTCATAGTGA
Found at i:1320 original size:22 final size:22
Alignment explanation
Indices: 1303--1425 Score: 158
Period size: 22 Copynumber: 5.6 Consensus size: 22
1293 AATCATACTT
*
1303 AGGTTATCAAAATTTCATAGTC
1 AGGTTACCAAAATTTCATAGTC
* **
1325 AAGTTACCAAAATTTCATAGGA
1 AGGTTACCAAAATTTCATAGTC
* *
1347 AGGTTACCAAAATATCATAGTG
1 AGGTTACCAAAATTTCATAGTC
**
1369 AGGTTA-CAAAATTTCATAGGG
1 AGGTTACCAAAATTTCATAGTC
*
1390 AGGTTACCAAAATTTTATAGTC
1 AGGTTACCAAAATTTCATAGTC
1412 AGGTTACCAAAATT
1 AGGTTACCAAAATT
1426 ATTATCGTTA
Statistics
Matches: 87, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
21 19 0.22
22 68 0.78
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.31
Consensus pattern (22 bp):
AGGTTACCAAAATTTCATAGTC
Found at i:1394 original size:43 final size:44
Alignment explanation
Indices: 1303--1425 Score: 185
Period size: 43 Copynumber: 2.8 Consensus size: 44
1293 AATCATACTT
* *
1303 AGGTTATCAAAATTTCATAGTCAAGTTACCAAAATTTCATAGGA
1 AGGTTACCAAAATTTCATAGTCAGGTTACCAAAATTTCATAGGA
* * *
1347 AGGTTACCAAAATATCATAGTGAGGTTA-CAAAATTTCATAGGG
1 AGGTTACCAAAATTTCATAGTCAGGTTACCAAAATTTCATAGGA
*
1390 AGGTTACCAAAATTTTATAGTCAGGTTACCAAAATT
1 AGGTTACCAAAATTTCATAGTCAGGTTACCAAAATT
1426 ATTATCGTTA
Statistics
Matches: 70, Mismatches: 8, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
43 39 0.56
44 31 0.44
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.31
Consensus pattern (44 bp):
AGGTTACCAAAATTTCATAGTCAGGTTACCAAAATTTCATAGGA
Found at i:1416 original size:65 final size:66
Alignment explanation
Indices: 1289--1424 Score: 184
Period size: 65 Copynumber: 2.1 Consensus size: 66
1279 CTAAAAAAAA
* * *
1289 AAAAAATCATACTTAGGTTATCAAAATTTCATAGTCAAGTTACCAAAATTTCATAGGAAGGTTAC
1 AAAATATCATACTGAGGTTATCAAAATTTCATAGGCAAGTTACCAAAATTTCATAGGAAGGTTAC
1354 C
66 C
* * * * **
1355 AAAATATCATAGTGAGGTTA-CAAAATTTCATAGGGAGGTTACCAAAATTTTATAGTCAGGTTAC
1 AAAATATCATACTGAGGTTATCAAAATTTCATAGGCAAGTTACCAAAATTTCATAGGAAGGTTAC
1419 C
66 C
1420 AAAAT
1 AAAAT
1425 TATTATCGTT
Statistics
Matches: 61, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
65 44 0.72
66 17 0.28
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.30
Consensus pattern (66 bp):
AAAATATCATACTGAGGTTATCAAAATTTCATAGGCAAGTTACCAAAATTTCATAGGAAGGTTAC
C
Found at i:2121 original size:331 final size:329
Alignment explanation
Indices: 1448--2166 Score: 804
Period size: 331 Copynumber: 2.2 Consensus size: 329
1438 TAATATATAT
* * * *
1448 TTTGATTAGGTGAATATAGATATTTCAAGG-GATCTCAGTGCCAAAAATCATTCAAAATTAACCG
1 TTTGATTAGATGAATATAGATATTTCAAGGAG-TCTC-GTGCCAAAAATCATGCAAAATGAACCA
* * *
1512 AGCTCCGGAACGCGTTTTTAGCCAAAAACAGTGATGATTATTACACGATTTCGGCTAAAATTTCC
64 AGCTCCGAAACGCGTTTTTAGCCAAAAACAGTGAT-ATAATTACACGATTTCGGCTAAAATTTCA
* * ** * * *
1577 CAAAATTGACCCGAAAGATATTTCCTCAATTTTTAGCCATAATACTAATAAAAATATATATAATT
128 AAAAATTAACCAAAAAGATATTTCCTCAATTTTTAGACAAAATACTAATAAAAAGATATATAATT
* * * *
1642 CAACGCCAAAAAGATTGAATGGCTTTTCACGCATTTAATATCGTTTTTCATATATTTTTTCTGAA
193 CAACACCAAAAAGATTGAAGGGATTTTCACGCATTTAATATCGTTTTTCA-ATATTTTTTCCGAA
* * * * *
1707 TTAATTTCTAATTAAATCGAAATAAGATTCAGATGCTCGTGAAAACAAATTCTTAAATGCAATGT
257 TTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGA
**
1772 GGTTAAGA
322 GACTAAGA
* * * *
1780 TTTTATTAGATGAATATAAATATTTCAAGGAGTGTCGGTGCCAAAAATCATGCAAAACTGAGCCA
1 TTTGATTAGATGAATATAGATATTTCAAGGAGTCTC-GTGCCAAAAATCATGCAAAA-TGAACCA
* * * * *
1845 AGGC-CATGAAACGTGTTTTTAGCCAAAAACCGTGAT-TAACTTACATGATTTTGGCTAAAATTT
64 A-GCTC-CGAAACGCGTTTTTAGCCAAAAACAGTGATATAA-TTACACGATTTCGGCTAAAA-TT
* * * * * *
1908 TGCAAAAAATTAATCAAAAAG-TTTTTCCTCAATTTTTGGATAAAATACTCAT-GAAAGATATAT
125 T-CAAAAAATTAACCAAAAAGATATTTCCTCAATTTTTAGACAAAATACTAATAAAAAGATATAT
* * *
1971 AATTCAACACCAAAAAGATTGAAGGGATTTTTACG-TTTCTAATATCGTTTTTC-CTATTTTTTC
189 AATTCAACACCAAAAAGATTGAAGGGATTTTCACGCATT-TAATATCGTTTTTCAATATTTTTTC
* * * *
2034 CGAATTAATTTCTAATTAAATTGAAACAATATTCAGATGCTTGTAAAAACAAATCCTTGAATCCA
253 CGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCA
*
2099 ATGAGACTGAGA
318 ATGAGACTAAGA
* * * * *
2111 TTTGATTAGATGAATATAGATATTTCAAGTAGTTTCGAGCTAAAAATTATGCAAAA
1 TTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGTGCCAAAAATCATGCAAAA
2167 AGATGCTTTT
Statistics
Matches: 323, Mismatches: 56, Indels: 18
0.81 0.14 0.05
Matches are distributed among these distances:
330 17 0.05
331 105 0.33
332 53 0.16
333 79 0.24
334 56 0.17
335 13 0.04
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (329 bp):
TTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGTGCCAAAAATCATGCAAAATGAACCAAG
CTCCGAAACGCGTTTTTAGCCAAAAACAGTGATATAATTACACGATTTCGGCTAAAATTTCAAAA
AATTAACCAAAAAGATATTTCCTCAATTTTTAGACAAAATACTAATAAAAAGATATATAATTCAA
CACCAAAAAGATTGAAGGGATTTTCACGCATTTAATATCGTTTTTCAATATTTTTTCCGAATTAA
TTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGAGACT
AAGA
Found at i:8489 original size:12 final size:12
Alignment explanation
Indices: 8472--8497 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
8462 CCGTCCCATA
8472 TTATCTGTCCAC
1 TTATCTGTCCAC
8484 TTATCTGTCCAC
1 TTATCTGTCCAC
8496 TT
1 TT
8498 TGGAGAAGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.31, G:0.08, T:0.46
Consensus pattern (12 bp):
TTATCTGTCCAC
Found at i:11139 original size:13 final size:13
Alignment explanation
Indices: 11121--11153 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
11111 TGCTTATGTC
11121 TTTTTTTTTGTTT
1 TTTTTTTTTGTTT
11134 TTTTTTTTTGTTT
1 TTTTTTTTTGTTT
*
11147 TTCTTTT
1 TTTTTTT
11154 GAAAATCTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.00, C:0.03, G:0.06, T:0.91
Consensus pattern (13 bp):
TTTTTTTTTGTTT
Found at i:18795 original size:16 final size:16
Alignment explanation
Indices: 18774--18805 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
18764 AAAAGAAAAT
18774 AAAAATAGAATATATG
1 AAAAATAGAATATATG
*
18790 AAAAATATAATATATG
1 AAAAATAGAATATATG
18806 TACACCAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.62, C:0.00, G:0.09, T:0.28
Consensus pattern (16 bp):
AAAAATAGAATATATG
Done.