Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011703.1 Corchorus olitorius cultivar O-4 contig11736, 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: 1874
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Found at i:281 original size:154 final size:154
Alignment explanation
Indices: 1--491 Score: 829
Period size: 154 Copynumber: 3.2 Consensus size: 154
1 TTCGATTTGGCAACCCTCAATGCTTTTCTTTCCAATGTTTATGGCCTAACTATAATCATTTTGGT
1 TTCGATTTGGCAACCCTCAATGCTTTTCTTTCCAATGTTTATGGCCTAACTATAATCATTTTGGT
* *
66 AAGATTAGTCCACTTTGAAGTTTTTAGATCTTTTGGAACACTTGTTATTTTGGGCATATCGAGGA
66 AAGATTAGTCCACTTTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCATATCGAGGA
*
131 CCATTAGTTCCGTTTTGAATCATC
131 CCATTAGTTCCGTTTTGAATCGTC
155 TTCGATTTGGCAACCCTCAATGCTTTTCTTTCCAATGTTTATGGCCTAACTATAATCATTTTGGT
1 TTCGATTTGGCAACCCTCAATGCTTTTCTTTCCAATGTTTATGGCCTAACTATAATCATTTTGGT
*
220 AAGATTAGTCCACTTTGAAGTTTTTAGCTCACTTGGAACACTTGTTATTTTGGGCATATCGAGGA
66 AAGATTAGTCCACTTTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCATATCGAGGA
285 CCATTAGTTCCGTTTTGAATCGTC
131 CCATTAGTTCCGTTTTGAATCGTC
* * * *
309 TTCGATTAGGCAAACCTCAATGCCTTTCTTTCCAATGTTTATGGCCTAACTATAATCATTTCGGT
1 TTCGATTTGGCAACCCTCAATGCTTTTCTTTCCAATGTTTATGGCCTAACTATAATCATTTTGGT
* * * * * *
374 AAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTTGAGCACTTGTTATTTTGGGCCTATCGGGGC
66 AAGATTAGTCCACTTTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCATATCGAGGA
*
439 CCATTAGTTCCGTTTTGATTCGTC
131 CCATTAGTTCCGTTTTGAATCGTC
* *
463 TTCAATTTGGCAACCCCCAATGCTTTTCT
1 TTCGATTTGGCAACCCTCAATGCTTTTCT
492 AATAATCATT
Statistics
Matches: 316, Mismatches: 21, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
154 316 1.00
ACGTcount: A:0.22, C:0.20, G:0.17, T:0.40
Consensus pattern (154 bp):
TTCGATTTGGCAACCCTCAATGCTTTTCTTTCCAATGTTTATGGCCTAACTATAATCATTTTGGT
AAGATTAGTCCACTTTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCATATCGAGGA
CCATTAGTTCCGTTTTGAATCGTC
Found at i:604 original size:133 final size:132
Alignment explanation
Indices: 360--608 Score: 365
Period size: 133 Copynumber: 1.9 Consensus size: 132
350 TGGCCTAACT
* * *
360 ATAATCATTTCGGTAAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTTGAGCACTTGTTATTTT
1 ATAATCATTTCGGTAAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTC
* * * ** *
425 GGGCCTATCGGGGCCCATTAGTTCCGTTTTGATTCGTCTTCAATTTGGCAACCCCCAATGCTTTT
66 GAGCCAATCGGGCCCCATTAGTGACGTTTTGAATCGTCTTCAATTT-GCAACCCCCAATGCTTTT
490 CTA
130 CTA
* *
493 ATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTC
1 ATAATCATTTCGGTAAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTC
*
558 GAGCCAATCGGGCCCCATTAGTGACGTTTTGAATC-TACTTCTATTTGCAAC
66 GAGCCAATCGGGCCCCATTAGTGACGTTTTGAATCGT-CTTCAATTTGCAAC
609 TTTTAATGCC
Statistics
Matches: 103, Mismatches: 12, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
132 6 0.06
133 97 0.94
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (132 bp):
ATAATCATTTCGGTAAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTC
GAGCCAATCGGGCCCCATTAGTGACGTTTTGAATCGTCTTCAATTTGCAACCCCCAATGCTTTTC
TA
Found at i:861 original size:191 final size:190
Alignment explanation
Indices: 501--886 Score: 530
Period size: 191 Copynumber: 2.0 Consensus size: 190
491 TAATAATCAT
* * * *
501 TTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTCGAGCCAAT
1 TTTGGTGAGATTAGTCCACTATGAAGTTTTTAACTCATATGAAACACTTGTTATTTCGAGCCAAT
* * * * * *
566 CGGGCCCCATTAGTGACGTTTTGAATCTACTTCTATTTGCAACTTTTAATGCCTTTCTTTCCATT
66 CGGGCCCCATTAGTCACGTTTTGAATCTACTTCGATTGGCAACTCTCAATGCCTTTCCTTCCATT
*
631 GTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTAAAGTTTTTAGCACA
131 GTTTATAGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTAAAGTTTTTAGCACA
* * * *
691 TTTGGTGAGATTAGTCCACTATGAGGTTTTTAACTCATATGAAACACATT-TTATTTTGGGCCTA
1 TTTGGTGAGATTAGTCCACTATGAAGTTTTTAACTCATATGAAACAC-TTGTTATTTCGAGCCAA
*
755 TCTGGG-CCCATTAGTTCA-GTTTTGAATCGT-CTTCGATTAGGCAAAC-CTCAATGCTTTTCCT
65 TC-GGGCCCCATTAG-TCACGTTTTGAATC-TACTTCGATT-GGC-AACTCTCAATGCCTTTCCT
*
816 TCCATTGTTTATAGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCAC
125 TCCATTGTTTATAGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTAAAGTTTTTAGCAC
881 A
190 A
882 TTTGG
1 TTTGG
887 AACACTTGTT
Statistics
Matches: 173, Mismatches: 17, Indels: 11
0.86 0.08 0.05
Matches are distributed among these distances:
190 80 0.46
191 90 0.52
192 3 0.02
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.40
Consensus pattern (190 bp):
TTTGGTGAGATTAGTCCACTATGAAGTTTTTAACTCATATGAAACACTTGTTATTTCGAGCCAAT
CGGGCCCCATTAGTCACGTTTTGAATCTACTTCGATTGGCAACTCTCAATGCCTTTCCTTCCATT
GTTTATAGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTAAAGTTTTTAGCACA
Found at i:1085 original size:154 final size:154
Alignment explanation
Indices: 691--1077 Score: 596
Period size: 154 Copynumber: 2.5 Consensus size: 154
681 TTTTAGCACA
* * * * * *
691 TTTGGTGAGATTAGTCCACTATGAGGTTTTTAACTCATATGAAACACATT-TTATTTTGGGCCTA
1 TTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCACATTTGGAACAC-TTGTTATTTTGGGCCTA
* * * * *
755 TCTGGGCCCATTAGTTCAGTTTTGAATCGTCTTCGATTAGGCAAACCTCAATGCTTTTCCTTCCA
65 TCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCA
*
820 TTGTTTATAGCCTAACTATAATCAT
130 TTGTTTATGGCCTAACTATAATCAT
845 TTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCACATTTGGAACACTTGTTATTTTGGGCCTAT
1 TTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCACATTTGGAACACTTGTTATTTTGGGCCTAT
* *
910 CGGGGCCCATTGGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTTAATGCTTTTCTTTCCAT
66 CGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCAT
* *
975 TGTTTATGGCCTAATTATTATCAT
131 TGTTTATGGCCTAACTATAATCAT
* *
999 TTTGGTGAGATTAGTCCAATGTGAAGTTTTTAGCACATTTGGAACACTTGTTATTTTGAGCCTAT
1 TTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCACATTTGGAACACTTGTTATTTTGGGCCTAT
1064 CGGGGCCCATTAGT
66 CGGGGCCCATTAGT
1078 GACGTTTTTG
Statistics
Matches: 213, Mismatches: 19, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
153 2 0.01
154 211 0.99
ACGTcount: A:0.22, C:0.18, G:0.19, T:0.40
Consensus pattern (154 bp):
TTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCACATTTGGAACACTTGTTATTTTGGGCCTAT
CGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAACCCTCAATGCTTTTCTTTCCAT
TGTTTATGGCCTAACTATAATCAT
Done.