Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012463.1 Corchorus capsularis cultivar CVL-1 contig12484, 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: 2447
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Found at i:1018 original size:321 final size:321
Alignment explanation
Indices: 1--2447 Score: 3568
Period size: 322 Copynumber: 7.7 Consensus size: 321
* * * * * *
1 GGATTTTTTTTATGAGCATGTGGATTTTGTTTCAATTTAATTAG-AATGTAATTCAGAAAAAAAT
1 GGATTTTTTTTACGAGCATCTGAATTTTGTTTCGATTTAATTAGAAAT-AAATTCAGTAAAAAAT
* * *
65 GGAAAAGCAATATTGGAAACGTGAAAAACCCTTCAATCTTTTCTGGCGTTGAATTATATACTTAT
65 GGAAAAACAATATTGGAAACGTGAAAAACCCTGCAATCTTTTTTGGCGTTGAATTATATACTT-T
* *
130 TCAGAGTGGTGTGG-AAAAAAA--AG--GAAAATTTTCCGGGTCAATTTTTAGCCAAAATCGTGT
129 TCAGAGTGGTGTGGCAAAAAAATGAGAAAAAAATTTT-CGGGTCAATTTTTAGCCGAAATCGTGT
* * * * *
190 AATAACCATCACGGTTTTTGGCTAAAAACGTGTTTCAGGGCCCCGACTCAGTTTTGCTTGATTTT
193 ACTAACCATCACGGTTTTTAGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTTTGCATGATTTT
*
255 TGGTAGAAAGACACCTTCAAATATCTATATTCATATAACCAAATCTCAGCTAATTTGGATTTAA
258 TGGTAGAAAGACACCTTCAAATATCTATATTCATATAACCAAATCTCAGCCAATTTGGATTTAA
* *
319 GGATTTGTTTTACGAGCATCTGAATTTTGTTTCGATTTAATTAGAAACAAATTCAGTAAAAAATG
1 GGATTTTTTTTACGAGCATCTGAATTTTGTTTCGATTTAATTAGAAATAAATTCAGTAAAAAATG
* *
384 GAAAAACAATATT-GATAACGTGAAAAACCCAGCAATCTTTTTTGGCTTTGAATTATATACTTAT
66 GAAAAACAATATTGGA-AACGTGAAAAACCCTGCAATCTTTTTTGGCGTTGAATTATATACTT-T
* * *
448 TCAGAGTGGTGTGGCCAAATAAAA--AG-TAAAAATTTCCAGGTCAATTTTTAGCCGAAATCGTG
129 TCAGAGTGGTGTGG-CAAA-AAAATGAGAAAAAAATTTTCGGGTCAATTTTTAGCCGAAATCGTG
* * * * *
510 TAATAACCATCACGGTTTTTTGGCTAAAAACGTGTTTCAGGGCCCCGACTCAGTTTTGCTTGATT
192 TACTAACCATCACGG-TTTTTAGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTTTGCATGATT
*
575 TTTGGTAGAAAGACACCTTCAAATATCTATATTCATATAACCAAATCTCAGCTAATTTGGATTTA
256 TTTGGTAGAAAGACACCTTCAAATATCTATATTCATATAACCAAATCTCAGCCAATTTGGATTTA
640 A
321 A
641 GGATTTTTTTTACGAGCATCTGAATTTTGTTTCGATTTAATTAGAAATAAATTCAGTAAAAAATG
1 GGATTTTTTTTACGAGCATCTGAATTTTGTTTCGATTTAATTAGAAATAAATTCAGTAAAAAATG
* * *
706 GAAAAGCAATATTGGAAACGTGAAAAACCCTTCAATCTTTTTTGTCGTTGAATTATATACTTTTC
66 GAAAAACAATATTGGAAACGTGAAAAACCCTGCAATCTTTTTTGGCGTTGAATTATATACTTTT-
* *
771 CTGAGTAGTGTGGCAAAAAAATGAGAAAAAAATTTTCGGGTCAATTTTTAGCCGAAATCGTGTAC
130 CAGAGTGGTGTGGCAAAAAAATGAGAAAAAAATTTTCGGGTCAATTTTTAGCCGAAATCGTGTAC
* * * *
836 TTA-TATCACGGTTTTTAGCTAAACACACGTTTCGGGGCCCCGACTCAGTTTTGCATGATTTTTG
195 TAACCATCACGGTTTTTAGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTTTGCATGATTTTTG
* *
900 GTAGAAAGACACCTTCAAGTATCTATATTCCTATAACCAAATCTCAGCCAATTTGGATTTAA
260 GTAGAAAGACACCTTCAAATATCTATATTCATATAACCAAATCTCAGCCAATTTGGATTTAA
* *
962 GGATTTTTTTTACGAGCATCTGAATTTTGTTTCGATTTAATTGGAAATAGATTCAGTAAAAAATG
1 GGATTTTTTTTACGAGCATCTGAATTTTGTTTCGATTTAATTAGAAATAAATTCAGTAAAAAATG
* * *
1027 GAAAAACAATATTGGTAACGTGAAAAACCCTGCAATCTTTTTT-GCTTTGAATTATATACATATT
66 GAAAAACAATATTGGAAACGTGAAAAACCCTGCAATCTTTTTTGGCGTTGAATTATATAC-TTTT
** * *
1091 CAGAGTGGTGTGGC-AAAAAA-G-GTGAAAAATTTTCCCGGGTCAGTTTTTAGCCGAAATCGTTT
130 CAGAGTGGTGTGGCAAAAAAATGAGAAAAAAATTTT--CGGGTCAATTTTTAGCCGAAATCGTGT
* * *
1153 ACTAACCATCACGGTTTTTGGCTAAAAACGTGTTTCAGGGCCCCGACTCAGTTTTGCATGATTTT
193 ACTAACCATCACGGTTTTTAGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTTTGCATGATTTT
*
1218 TGGTAGAAAGACACCTTCAAATATCTATATTCATATAACCAAATCTCAGCTAATTTGGATTTAA
258 TGGTAGAAAGACACCTTCAAATATCTATATTCATATAACCAAATCTCAGCCAATTTGGATTTAA
1282 GGA-TTTTTTTACGAGCATCTGAATTTTGTTTCGATTTAATTAGAAATAAATTCAGTAAAAAATG
1 GGATTTTTTTTACGAGCATCTGAATTTTGTTTCGATTTAATTAGAAATAAATTCAGTAAAAAATG
* * *
1346 GAAAAACAATATTGGAAGCGTGAAAAACCCTTCAATCTTTTTTGTCGTTGAATTATATACTTTTC
66 GAAAAACAATATTGGAAACGTGAAAAACCCTGCAATCTTTTTTGGCGTTGAATTATATACTTTT-
* * *
1411 CTGAGTAGTGTGGCAAAAAAATGAGAAAAAAACTTTTCAGGTCAATTTTTAGCCGAAATCGTGTA
130 CAGAGTGGTGTGGCAAAAAAATGAGAAAAAAA-TTTTCGGGTCAATTTTTAGCCGAAATCGTGTA
* * * *
1476 CTTA-TATCACGGTTTTTAGCTAAACACGCGTTTCGGGTCCCCGACTCAGTTTTGCATGATTTTT
194 CTAACCATCACGGTTTTTAGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTTTGCATGATTTTT
*
1540 GCTAGAAAGACACCTTCAAATATCTATATTCATATAACCAAATCTCAGCCAATTTGGATTTAA
259 GGTAGAAAGACACCTTCAAATATCTATATTCATATAACCAAATCTCAGCCAATTTGGATTTAA
* *
1603 GGATTTTTTTGACGAGCATCTGAATTTTGTTTCGATTTAATTAGAAATAAATTCAGTAAAAACTG
1 GGATTTTTTTTACGAGCATCTGAATTTTGTTTCGATTTAATTAGAAATAAATTCAGTAAAAAATG
* *
1668 GAAAAACAATATTGGTAACGTGAAAAACCCTGCAATCTTTTTTGGCGTTGATTTATATACTTATT
66 GAAAAACAATATTGGAAACGTGAAAAACCCTGCAATCTTTTTTGGCGTTGAATTATATACTT-TT
* *
1733 CAGAGTGGTGTGGCTAAAAAAGGAGAAAAAAATTTTCGGGTCAATTTTTAGCCGAAATCGTGTAC
130 CAGAGTGGTGTGGCAAAAAAATGAGAAAAAAATTTTCGGGTCAATTTTTAGCCGAAATCGTGTAC
* * * *
1798 TAACCTTCACGGTTTTTGGCTAAAAACGCGTTTCGGGGCCCCGACTCGGTTTTGAATGATTTTTG
195 TAACCATCACGGTTTTTAGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTTTGCATGATTTTTG
*
1863 GTAGAAAGACACCTTCAAATATCTATATTCATATAACAAAATCTCAGCCAATTTGGATTTAA
260 GTAGAAAGACACCTTCAAATATCTATATTCATATAACCAAATCTCAGCCAATTTGGATTTAA
* *
1925 TGATTTTTTTTTTACGAGCATCTGAATTTTGTTTCGATTTAATTAGAAATAAATTCAAGAAAAAA
1 GGA--TTTTTTTTACGAGCATCTGAATTTTGTTTCGATTTAATTAGAAATAAATTC-AGTAAAAA
* *
1990 ATGGAAAAACAATATTGTAAACGTGAAAAACCCTGCAATCTTTTCTGGCGTTG-A--AT-TA---
63 ATGGAAAAACAATATTGGAAACGTGAAAAACCCTGCAATCTTTTTTGGCGTTGAATTATATACTT
* * * *
2048 -T--GAGTGTTGTGGC-AAAAAATGAGAAAAAAAATTTCGGGTTAATTTTTAGCTGAAATCGTGT
128 TTCAGAGTGGTGTGGCAAAAAAATGAGAAAAAAATTTTCGGGTCAATTTTTAGCCGAAATCGTGT
* * *
2109 AGTAACCATAACGGTTTTTAGCTAAAAACGCGTTTCGGGGCCCCGACCCAGTTTTGCATGATTTT
193 ACTAACCATCACGGTTTTTAGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTTTGCATGATTTT
*
2174 TGGTAGAAAGACACCTTCAAATATCTATATTCATATAACGAAATCTCAGCCAATTTGGATTTAA
258 TGGTAGAAAGACACCTTCAAATATCTATATTCATATAACCAAATCTCAGCCAATTTGGATTTAA
** * *
2238 TAATTTTTTTTACGAGCATCTGAATTTTGTTTCGATTTAATTAGTAATAAATTCAAGAAAAAAAA
1 GGATTTTTTTTACGAGCATCTGAATTTTGTTTCGATTTAATTAGAAATAAATTC-AG-TAAAAAA
* *
2303 TGGAAAAACAATATTGTAAACGTGAAAAACCCTTCAATCTTTTTTGGCGTTG-A--AT-TA----
64 TGGAAAAACAATATTGGAAACGTGAAAAACCCTGCAATCTTTTTTGGCGTTGAATTATATACTTT
* *
2360 T--GAGTGGTGTGGC-AAAAAATGAGAAAAAAATTTTCGGGTTAATTTTTAGCTGAAATCGTGTA
129 TCAGAGTGGTGTGGCAAAAAAATGAGAAAAAAATTTTCGGGTCAATTTTTAGCCGAAATCGTGTA
*
2422 GTAACCATCACGGTTTTTAGCTAAAA
194 CTAACCATCACGGTTTTTAGCTAAAA
Statistics
Matches: 1961, Mismatches: 139, Indels: 64
0.91 0.06 0.03
Matches are distributed among these distances:
311 53 0.03
312 147 0.07
313 167 0.09
314 11 0.01
316 1 0.00
317 12 0.01
318 125 0.06
319 139 0.07
320 176 0.09
321 423 0.22
322 550 0.28
323 47 0.02
324 54 0.03
325 56 0.03
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (321 bp):
GGATTTTTTTTACGAGCATCTGAATTTTGTTTCGATTTAATTAGAAATAAATTCAGTAAAAAATG
GAAAAACAATATTGGAAACGTGAAAAACCCTGCAATCTTTTTTGGCGTTGAATTATATACTTTTC
AGAGTGGTGTGGCAAAAAAATGAGAAAAAAATTTTCGGGTCAATTTTTAGCCGAAATCGTGTACT
AACCATCACGGTTTTTAGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTTTGCATGATTTTTGG
TAGAAAGACACCTTCAAATATCTATATTCATATAACCAAATCTCAGCCAATTTGGATTTAA
Done.