Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011729.1 Corchorus olitorius cultivar O-4 contig11762, 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: 1899
ACGTcount: A:0.21, C:0.20, G:0.18, T:0.40
Found at i:289 original size:154 final size:154
Alignment explanation
Indices: 1--1899 Score: 2788
Period size: 154 Copynumber: 12.2 Consensus size: 154
* *
1 ACTTGTTATTTTAGGCATATCGAGGACCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACC
1 ACTTGTTATTTTGGGCATATCGAGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACC
* * *
66 CTCAATGCTTTTCTCTCCAATGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTT
66 CTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTG
*
131 TGAAGTTTTTAGCTCAATTGGAAC
131 TGAAGTTTTTAGCTCATTTGGAAC
* *
155 ACTCGTTATTTTGGGCATATCGAGGACCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACC
1 ACTTGTTATTTTGGGCATATCGAGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACC
*
220 CTCAATGCTTTTCGTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTG
66 CTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTG
285 TGAAGTTTTTAGCTCATTTGGAAC
131 TGAAGTTTTTAGCTCATTTGGAAC
* **
309 ACTTGTTATTTTGGGCATATCGAGGACCATTTCTTCCGTTTTGAATCGTCTTCGATTTGGCAACC
1 ACTTGTTATTTTGGGCATATCGAGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACC
* * *
374 CTCAATGCTTTTCGTTCCAATTGTTTATGGCCTAACAATAATCATTTTGGTGAGATTAGCCCACT
66 CTCAATGCTTTTCTTTCC-ATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACT
* * * *
439 GTGAATTTTTTGGTTCATTCGGAAC
130 GTGAAGTTTTTAGCTCATTTGGAAC
* * *
464 ACTTTTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACC
1 ACTTGTTATTTTGGGCATATCGAGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACC
* *
529 CTCAATGCTTTTCTTTCCAATGTTTATGGCCTAACTATAATCATTTTGGTAAGATTAGTCCACT-
66 CTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTG
593 TGGAAGTTTTTAGCTCATTTGGAAC
131 T-GAAGTTTTTAGCTCATTTGGAAC
* *
618 ACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACC
1 ACTTGTTATTTTGGGCATATCGAGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACC
* *
683 CTCAATGCTTTTCTTTCCAATGTTTATAGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTG
66 CTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTG
* *
748 TTAAGTTTTTAGCTCAATTGGAAC
131 TGAAGTTTTTAGCTCATTTGGAAC
* * * * *
772 ACTCGTTATTTTAGGCATATCGAGGACCATTAGTTCCGTCTTGAATTGTCTTCGATTTGGCAACC
1 ACTTGTTATTTTGGGCATATCGAGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACC
* * *
837 CTCAATGCTTTTCTTTCCAATGTTTATAGCCTAACTATAATCATTTTGGTAAGATTAGTCCACTG
66 CTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTG
*
902 TGAAGTTTTTAGCTCACTTGGAAC
131 TGAAGTTTTTAGCTCATTTGGAAC
*
926 ACTTGTTATTTTGGGCATATCGAGGACCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACC
1 ACTTGTTATTTTGGGCATATCGAGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACC
* *
991 CTCAATGCTTTTCCTTCCATTGTTTATGGCCTAACTATAATCATTTTGGAGAGATTAGTCCACTG
66 CTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTG
* * *
1056 TGAAGTTTTTAGCTTACTTGCAAC
131 TGAAGTTTTTAGCTCATTTGGAAC
* * *
1080 ACTTGTTATTTTGGGCATATCGAGGACCATTAGTTCCGTTTTGAATCGTCTTGGATTTGGCAAAC
1 ACTTGTTATTTTGGGCATATCGAGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACC
*
1145 CTCAATGCTTTTCTTTCCAATT-TTTATGGCCTAACTATAATCATTTTGGAGAGATTAGTCCACT
66 CTCAATGCTTTTCTTTCC-ATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACT
* *
1209 TTGAAGTTTTTTTG-TCATTTGGAAC
130 GTGAAG-TTTTTAGCTCATTTGGAAC
*
1234 ACTTGTTATTTTGGGCCTATC-AGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAC
1 ACTTGTTATTTTGGGCATATCGA-GGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAC
*
1298 CCTCAACTGCTTTTCTTTCCATTGTTTA-GGCCTAACTATAATCATTTTGGTAAGTATTAGTCCT
65 CCTCAA-TGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAG-ATTAGTCC-
* *
1362 ACTTTGAAGTTTTTTTG-TCATTTGGAAC
127 ACTGTGAAG-TTTTTAGCTCATTTGGAAC
* *
1390 ACTTTGGTTATTTTGGGCCTATCGGGGGCCCCATTAGTTCCGTTTTTGAATCGTCTTCGATTTGG
1 AC-TT-GTTATTTTGGGCATATC-GAGG-CCCATTAGTTCCG-TTTTGAATCGTCTTCGATTTGG
1455 CAACCCCTCAAATGCGTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTA
61 CAA-CCCTC-AATGC-TTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTA
*
1520 GTCCACTGTGAATTTTTTAGCTCATTTGGAAC
123 GTCCACTGTGAAGTTTTTAGCTCATTTGGAAC
* *
1552 TACTTCGTTATTTTGGGCCGTACTC-AGGGCCCTATTAGTTCC-ATTTGAATCGTCTTCGATTTG
1 -ACTT-GTTATTTTGGG-CATA-TCGA-GGCCC-ATTAGTTCCGTTTTGAATCGTCTTCGATTTG
* * * *
1615 GCAACCCTCAATGCTTTCCGTTCCATCGTTTATGGCCTAACTATAATCATTTTGGTCAGATTAGT
60 GCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGT
* * * * *
1680 CCACTGTGAATTTTTTGGTTCACTAGGAAC
125 CCACTGTGAAGTTTTTAGCTCATTTGGAAC
* * * * ** *
1710 ACTTTTTATTTTGGCCCTATCGGGGCCCATTAGTGACGTTTTGAATCATCTTCGATTTGGCAACC
1 ACTTGTTATTTTGGGCATATCGAGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACC
* *
1775 CTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGGTTAGTCCACTT
66 CTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTG
1840 TGAAGTTTTTTAGCTTCAATTTGGAAC
131 TGAAG-TTTTTAGC-TC-ATTTGGAAC
* *
1867 ACTTGTTATTTTGGGCCTATCGGGGCCCATTAG
1 ACTTGTTATTTTGGGCATATCGAGGCCCATTAG
Statistics
Matches: 1605, Mismatches: 109, Indels: 59
0.91 0.06 0.03
Matches are distributed among these distances:
153 9 0.01
154 1043 0.65
155 185 0.12
156 41 0.03
157 44 0.03
158 90 0.06
159 7 0.00
160 18 0.01
161 55 0.03
162 42 0.03
163 44 0.03
164 27 0.02
ACGTcount: A:0.21, C:0.20, G:0.18, T:0.40
Consensus pattern (154 bp):
ACTTGTTATTTTGGGCATATCGAGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACC
CTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTG
TGAAGTTTTTAGCTCATTTGGAAC
Found at i:1311 original size:617 final size:616
Alignment explanation
Indices: 1--1899 Score: 2974
Period size: 617 Copynumber: 3.1 Consensus size: 616
* * * *
1 ACTTGTTATTTTAGGCATATCGAGGACCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACC
1 ACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACC
*
66 CTCAATGCTTTTCTCTCCAATGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTT
66 CTCAATGCTTTTCTTTCCAATGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTT
131 TGAAGTTTTTAGCTCAATTGGAACACTCGTTATTTTGGGCATATCGAGGACCATTAGTTCCGTTT
131 TGAAGTTTTTAGCTCAATTGGAACACTCGTTATTTTGGGCATATCGAGGACCATTAGTTCCGTTT
*
196 TGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCGTTCCATTGTTTATGGCCTAACTATAAT
196 TGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAAT
261 CATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCA
261 CATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCA
** *
326 TATCGAGGACCATTTCTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCGTTC
326 TATCGAGGACCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCCTTC
* *
391 CAATTGTTTATGGCCTAACAATAATCATTTTGGTGAGATTAGCCCACTGTGAATTTTTTGGTT-C
391 C-ATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAATTTTTTGGTTAC
455 ATTCGGAACACTTTTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGAT
455 -TT-GGAACACTTTTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGAT
*
520 TTGGCAACCCTCAATGCTTTTCTTTCCAATGTTTATGGCCTAACTATAATCATTTTGGTA-AGAT
518 TTGGCAACCCTCAATGCTTTTCTTTCCAATTTTTATGGCCTAACTATAATCATTTTGG-AGAGAT
*
584 TAGTCCACTTGGAAG-TTTTTAGCTCATTTGGAAC
582 TAGTCCACTTTGAAGTTTTTTAGCTCATTTGGAAC
618 ACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACC
1 ACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACC
*
683 CTCAATGCTTTTCTTTCCAATGTTTATAGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTG
66 CTCAATGCTTTTCTTTCCAATGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACT-
* *
748 TT-AAGTTTTTAGCTCAATTGGAACACTCGTTATTTTAGGCATATCGAGGACCATTAGTTCCGTC
130 TTGAAGTTTTTAGCTCAATTGGAACACTCGTTATTTTGGGCATATCGAGGACCATTAGTTCCGTT
* * *
812 TTGAATTGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCAATGTTTATAGCCTAACTATAA
195 TTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAA
* *
877 TCATTTTGGTAAGATTAGTCCACTGTGAAGTTTTTAGCTCACTTGGAACACTTGTTATTTTGGGC
260 TCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGC
942 ATATCGAGGACCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCCTT
325 ATATCGAGGACCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCCTT
* * *
1007 CCATTGTTTATGGCCTAACTATAATCATTTTGGAGAGATTAGTCCACTGTGAAGTTTTTAGCTTA
390 CCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAA-TTTTTTGGTTA
* * * * * *
1072 CTTGCAACACTTGTTATTTTGGGCATATCGAGGACCATTAGTTCCGTTTTGAATCGTCTTGGATT
454 CTTGGAACACTTTTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATT
*
1137 TGGCAAACCTCAATGCTTTTCTTTCCAATTTTTATGGCCTAACTATAATCATTTTGGAGAGATTA
519 TGGCAACCCTCAATGCTTTTCTTTCCAATTTTTATGGCCTAACTATAATCATTTTGGAGAGATTA
*
1202 GTCCACTTTGAAGTTTTTTTG-TCATTTGGAAC
584 GTCCACTTTGAAGTTTTTTAGCTCATTTGGAAC
*
1234 ACTTGTTATTTTGGGCCTATCAGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACC
1 ACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACC
* *
1299 CTCAACTGCTTTTCTTTCCATTGTTTA-GGCCTAACTATAATCATTTTGGTAAGTATTAGTCCTA
66 CTCAA-TGCTTTTCTTTCCAATGTTTATGGCCTAACTATAATCATTTTGGTGAG-ATTAGTCC-A
* * * * * *
1363 CTTTGAAGTTTTTTTG-TCATTTGGAACACTTTGGTTATTTTGGGCCTATCGGGGGCCCCATTAG
128 CTTTGAAG-TTTTTAGCTCAATTGGAACAC--TCGTTATTTTGGGCATATC-GAGG-ACCATTAG
1427 TTCCGTTTTTGAATCGTCTTCGATTTGGCAACCCCTCAAATGCGTTTTCTTTCCATTGTTTATGG
188 TTCCG-TTTTGAATCGTCTTCGATTTGGCAA-CCCTC-AATGC-TTTTCTTTCCATTGTTTATGG
*
1492 CCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAATTTTTTAGCTCATTTGGAACTACTT
249 CCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAAC-ACTT
* * *
1557 CGTTATTTTGGGCCGTACTC-AGGGCCCTATTAGTTCC-ATTTGAATCGTCTTCGATTTGGCAAC
313 -GTTATTTTGGG-CATA-TCGA-GGACC-ATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAC
* *
1620 CCTCAATGC-TTTCCGTTCCATCGTTTATGGCCTAACTATAATCATTTTGGTCAGATTAGTCCAC
373 CCTCAATGCTTTTCC-TTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCAC
* * **
1684 TGTGAATTTTTTGGTTCACTAGGAACACTTTTTATTTTGGCCCTATCGGGGCCCATTAGTGACGT
437 TGTGAATTTTTTGGTT-ACTTGGAACACTTTTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGT
*
1749 TTTGAATCATCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCC-ATTGTTTATGGCCTAACTAT
501 TTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCAATT-TTTATGGCCTAACTAT
* *
1813 AATCATTTTGGTGAGGTTAGTCCACTTTGAAGTTTTTTAGCTTCAATTTGGAAC
565 AATCATTTTGGAGAGATTAGTCCACTTTGAAGTTTTTTAGC-TC-ATTTGGAAC
1867 ACTTGTTATTTTGGGCCTATCGGGGCCCATTAG
1 ACTTGTTATTTTGGGCCTATCGGGGCCCATTAG
Statistics
Matches: 1178, Mismatches: 74, Indels: 44
0.91 0.06 0.03
Matches are distributed among these distances:
615 1 0.00
616 281 0.24
617 417 0.35
618 21 0.02
619 6 0.01
620 16 0.01
621 3 0.00
622 12 0.01
623 23 0.02
624 5 0.00
625 5 0.00
626 76 0.06
627 4 0.00
628 11 0.01
629 20 0.02
630 225 0.19
631 9 0.01
632 2 0.00
633 41 0.03
ACGTcount: A:0.21, C:0.20, G:0.18, T:0.40
Consensus pattern (616 bp):
ACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACC
CTCAATGCTTTTCTTTCCAATGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTT
TGAAGTTTTTAGCTCAATTGGAACACTCGTTATTTTGGGCATATCGAGGACCATTAGTTCCGTTT
TGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAAT
CATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCA
TATCGAGGACCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCCTTC
CATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAATTTTTTGGTTACT
TGGAACACTTTTTATTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTG
GCAACCCTCAATGCTTTTCTTTCCAATTTTTATGGCCTAACTATAATCATTTTGGAGAGATTAGT
CCACTTTGAAGTTTTTTAGCTCATTTGGAAC
Done.