Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013847.1 Corchorus olitorius cultivar O-4 contig13880, 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: 9906
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Found at i:7948 original size:13 final size:14
Alignment explanation
Indices: 7922--7950 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
7912 AAGTTCAACA
7922 ATAAAACTTAATTC
1 ATAAAACTTAATTC
7936 ATAAAAC-TAATTC
1 ATAAAACTTAATTC
7949 AT
1 AT
7951 GGAACATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (14 bp):
ATAAAACTTAATTC
Found at i:8520 original size:994 final size:994
Alignment explanation
Indices: 6486--8720 Score: 3614
Period size: 994 Copynumber: 2.2 Consensus size: 994
6476 CTACACCCTT
6486 TGGTGCCATCATGCTTGTCATTGTTGGCTGATGAAAAAAAAAAAAAAACTACAGCAGTTGAATTT
1 TGGTGCCATCATGCTTGTCATTGTTGGCTGAT--AAAAAAAAAAAAAA-TACAGCAGTTGAATTT
6551 ACACCCATTTTCTGGTAAAAGACACATAAAGGAAGTAAATGGAGAAAGCTTACCATCCCTTCAGT
63 ACACCCATTTTCTGGTAAAAGACACATAAAGGAAGTAAATGGAGAAAGCTTACCATCCCTTCAGT
* * * *
6616 CCCTTGAGCAGGTGGAGCAGTTTGATTTTCCTAATGAACAACAAAGGAAAATATAGGGACAACAC
128 CCCTTGAGCAGGTGGAGCAGTTTCATTTTCCTAGTGAACAACAAAGGAAAATATAGGGACAATAA
6681 GCAAACTTACAATCAAATGTAGAGCCTATGACTAATCAACAACCTAAATAAAAAATGGAAAAATA
193 GCAAACTTACAATCAAATGTAGAGCCTATGACTAATCAACAACCTAAATAAAAAATGGAAAAATA
*
6746 AGCAATGGAACTTGACTGCAATATGTTTAATAGTAATATATTCTTTCAAGTAGAATTCTAAGTAG
258 AACAATGGAACTTGACTGCAATATGTTTAATAGTAATATATTCTTTCAAGTAGAATTCTAAGTAG
* * *
6811 AAGTTCATCAGTAATATGTTTAACAGAAATGAATAGGCAAACAATACTACAAACAAAAGGACCTA
323 AAATTCATCAGTAATATGTTTAAAAGAAATGAATAGGCAAACAATACTACAAACAAAAGGACCAA
*
6876 AAAACACCATAAAGAACACTCTCACAGTTCGAGAATACTTAAAAGTTCAACAACAAAACTTAATT
388 AAAAAACCATAAAGAACACTCTCACAGTTCGAGAATACTTAAAAGTTCAACAACAAAACTTAATT
*
6941 CATAAAACCAATTCAAGGAACATAAATAATATGCTTAAATAATAAAACTATCCAGCATGCATCAC
453 CATAAAACCAATTCAAGGAACATAAATAATATGCTTAAATAATAAAACTATCCAGCACGCATCAC
* **
7006 CTAGTTAAACAAGTGGGTTTTTAAATGAACTTCACCAAGCGGGTCATGATTCATGGTGACTTAGA
518 CTAATTAAACAAGTGGGCATTTAAATGAACTTCACCAAGCGGGTCATGATTCATGGTGACTTAGA
** *
7071 TATAAAAAGTTCTAGAATTGAAGGATAAGAAACACATCTGTACACCTTAATGATGGGACTAACTA
583 TATAAAAAGTTCTAGAACCGAAGGATAAGAAACACATCTGCACACCTTAATGATGGGACTAACTA
* *
7136 CTAGAAGCATATATTATGGTTAAAAACACAGCCTTCCCAATCACAAGTTACTTTACAGTAAAATT
648 CTAGAAGCATATATAATGGTCAAAAACACAGCCTTCCCAATCACAAGTTACTTTACAGTAAAATT
** *
7201 CTAAGTTGAATGAAAATTCTAAGAAATTTAGAAAATCTGTAAGGAGTTAAAAGTTAGCCAAGGGA
713 CTAAGTAAAATGAAAAATCTAAGAAATTTAGAAAATCTGTAAGGAGTTAAAAGTTAGCCAAGGGA
* * **
7266 GGGTAACCAGAGAAGAAACATGGTAATCAATCCCTACAAGGCTGGGTTAAATTCCCATAAAATGT
778 GGGTAACCAAAGAAGAAACATGGTAATCAATCCCTAAAAAACTGGGTTAAATTCCCATAAAATGT
* * *
7331 GAGATAAGGGGAAAAAGAAGCTACAACAGTAGAATCTACACCCTTTCTCTGGTAAAACAGAGATG
843 GAGAGAAGGGAAAAAAGAAGCTACAACAGTAGAATCTACACCCATTCTCTGGTAAAACAGAGATG
* *
7396 AAGTAAAAGGAGAAAGCTTACCATCAATTGAGTCTCTTGAGTCCCTCGACCAGTTTCTGTTGGTG
908 AAGTAAAAGGAGAAAGCTTACAATCAATTGAGTCTCTTGAGTCCCTAGACCAGTTTCTGTTGGTG
7461 ATGCAGGTGTTGGAGGTCTAGA
973 ATGCAGGTGTTGGAGGTCTAGA
* ** *
7483 TGGTGCCAACATGCTTGTCATTGTTGGCTGATGCAAAAAAAAAAAATACAGCAATTGAATTTACA
1 TGGTGCCATCATGCTTGTCATTGTTGGCTGATAAAAAAAAAAAAAATACAGCAGTTGAATTTACA
*
7548 CCCATTTTCTGGTAAAAAACACATAAAGGAAGTAAATGGAGAAAGCTTACCATCCCTTCAGTCCC
66 CCCATTTTCTGGTAAAAGACACATAAAGGAAGTAAATGGAGAAAGCTTACCATCCCTTCAGTCCC
7613 TTGAGCAGGTGGAGCAGTTTCATTTTCCTAGTGAACAACAAAGGAAAATATAGGGACAATAAGCA
131 TTGAGCAGGTGGAGCAGTTTCATTTTCCTAGTGAACAACAAAGGAAAATATAGGGACAATAAGCA
* *
7678 AACTTACAATCAAATGTAGAGCCTATGACTAATCAACAACCTAAATAAAAAATTGAAAGATAAAC
196 AACTTACAATCAAATGTAGAGCCTATGACTAATCAACAACCTAAATAAAAAATGGAAAAATAAAC
*
7743 AATGGAACTTGACTGCAGTATGTTTAATAGTAATATATTCTTTCAAGTAGAATTCTAAGTAGAAA
261 AATGGAACTTGACTGCAATATGTTTAATAGTAATATATTCTTTCAAGTAGAATTCTAAGTAGAAA
* * *
7808 TTCATCAGTAATATGTTTAAAAGAAATGTATAGGCAAACAGTACTATAAACAAAAGGACCAAAAA
326 TTCATCAGTAATATGTTTAAAAGAAATGAATAGGCAAACAATACTACAAACAAAAGGACCAAAAA
*
7873 AAACCATAAAGAACACTCTCACAGTTCGAGAATACTTAAAAGTTCAACAATAAAACTTAATTCAT
391 AAACCATAAAGAACACTCTCACAGTTCGAGAATACTTAAAAGTTCAACAACAAAACTTAATTCAT
* * * * *
7938 AAAACTAATTCATGGAACATAAATAATATTCTTAAATAATAAAATTATCTAGCACGCATCACCTA
456 AAAACCAATTCAAGGAACATAAATAATATGCTTAAATAATAAAACTATCCAGCACGCATCACCTA
* * *
8003 ATTAAACAAGTGGGCATTTAAATGAATTTCACCAAGTGGGTCATGGATTTATGGTGACTTAGATA
521 ATTAAACAAGTGGGCATTTAAATGAACTTCACCAAGCGGGTCAT-GATTCATGGTGACTTAGATA
* * * *
8068 T-AAAAGTTCTGGAACCGAAGGATAAGAAACTCATTTGCAGACCTTAATGATGGGACTAACTACT
585 TAAAAAGTTCTAGAACCGAAGGATAAGAAACACATCTGCACACCTTAATGATGGGACTAACTACT
* *
8132 AGAAGCATATATAATGGTCAAAAACATAGCCTTCCC-ATCACAAGTTACTTTATAGTAAAATTCT
650 AGAAGCATATATAATGGTCAAAAACACAGCCTTCCCAATCACAAGTTACTTTACAGTAAAATTCT
* * * * *
8196 AAGTAAAATGAAAAATCTAAGAGATTTAGAATATCTGTAATGAGTTAAAAGTTAGCTAATGGAGG
715 AAGTAAAATGAAAAATCTAAGAAATTTAGAAAATCTGTAAGGAGTTAAAAGTTAGCCAAGGGAGG
* *
8261 GTAACCAAAGAAGGAACATGGTAATCAATCCCTAAAAAACTGGGTTCAATTCCCATAAAATGTGA
780 GTAACCAAAGAAGAAACATGGTAATCAATCCCTAAAAAACTGGGTTAAATTCCCATAAAATGTGA
* *
8326 GAGAAGGGAAAAAAGAAGCTACAACAGTGGAATCTACACCCATTCTCTGGTAAAAGAGAGATGAA
845 GAGAAGGGAAAAAAGAAGCTACAACAGTAGAATCTACACCCATTCTCTGGTAAAACAGAGATGAA
* * *
8391 GTAAATGGAGAAAGCTTACAATCGATTGAGTCTCTT-ACGTCCCTAGAGCAGTTTCTGTTGGTGA
910 GTAAAAGGAGAAAGCTTACAATCAATTGAGTCTCTTGA-GTCCCTAGACCAGTTTCTGTTGGTGA
* * *
8455 TGCAGTTGTTGGTGGTTTAGA
974 TGCAGGTGTTGGAGGTCTAGA
** * * * * ** *
8476 TGGTGTTATCATGTTTGTCGA-TGTTGGCTGATTAAAAGAAAAAAACTGTAGTAGTTGAATTTAC
1 TGGTGCCATCATGCTTGTC-ATTGTTGGCTGATAAAAAAAAAAAAAATACAGCAGTTGAATTTAC
*
8540 ACCCATTTTCTGGTAAAAGACACATAAAGAAAGTAAATGGAGAAAGCTTACCATCCCTTCAGTCC
65 ACCCATTTTCTGGTAAAAGACACATAAAGGAAGTAAATGGAGAAAGCTTACCATCCCTTCAGTCC
* * * *
8605 CTTGAGCAGGTGGACCAGTTTCATTTTCCTAGTGAAGAACAAAGGAAAATATAGAGACAATGAGC
130 CTTGAGCAGGTGGAGCAGTTTCATTTTCCTAGTGAACAACAAAGGAAAATATAGGGACAATAAGC
*
8670 AAACTTACAATCAAATGTAGAGCCTATGACTAATTAACAACCTAAATAAAA
195 AAACTTACAATCAAATGTAGAGCCTATGACTAATCAACAACCTAAATAAAA
8721 TAGCCTCTCG
Statistics
Matches: 1145, Mismatches: 90, Indels: 10
0.92 0.07 0.01
Matches are distributed among these distances:
992 1 0.00
993 502 0.44
994 579 0.51
995 32 0.03
997 31 0.03
ACGTcount: A:0.41, C:0.16, G:0.18, T:0.26
Consensus pattern (994 bp):
TGGTGCCATCATGCTTGTCATTGTTGGCTGATAAAAAAAAAAAAAATACAGCAGTTGAATTTACA
CCCATTTTCTGGTAAAAGACACATAAAGGAAGTAAATGGAGAAAGCTTACCATCCCTTCAGTCCC
TTGAGCAGGTGGAGCAGTTTCATTTTCCTAGTGAACAACAAAGGAAAATATAGGGACAATAAGCA
AACTTACAATCAAATGTAGAGCCTATGACTAATCAACAACCTAAATAAAAAATGGAAAAATAAAC
AATGGAACTTGACTGCAATATGTTTAATAGTAATATATTCTTTCAAGTAGAATTCTAAGTAGAAA
TTCATCAGTAATATGTTTAAAAGAAATGAATAGGCAAACAATACTACAAACAAAAGGACCAAAAA
AAACCATAAAGAACACTCTCACAGTTCGAGAATACTTAAAAGTTCAACAACAAAACTTAATTCAT
AAAACCAATTCAAGGAACATAAATAATATGCTTAAATAATAAAACTATCCAGCACGCATCACCTA
ATTAAACAAGTGGGCATTTAAATGAACTTCACCAAGCGGGTCATGATTCATGGTGACTTAGATAT
AAAAAGTTCTAGAACCGAAGGATAAGAAACACATCTGCACACCTTAATGATGGGACTAACTACTA
GAAGCATATATAATGGTCAAAAACACAGCCTTCCCAATCACAAGTTACTTTACAGTAAAATTCTA
AGTAAAATGAAAAATCTAAGAAATTTAGAAAATCTGTAAGGAGTTAAAAGTTAGCCAAGGGAGGG
TAACCAAAGAAGAAACATGGTAATCAATCCCTAAAAAACTGGGTTAAATTCCCATAAAATGTGAG
AGAAGGGAAAAAAGAAGCTACAACAGTAGAATCTACACCCATTCTCTGGTAAAACAGAGATGAAG
TAAAAGGAGAAAGCTTACAATCAATTGAGTCTCTTGAGTCCCTAGACCAGTTTCTGTTGGTGATG
CAGGTGTTGGAGGTCTAGA
Done.